Workshop on mobile laboratories deployed in the Ebola outbreak in West-Africa 2014-2015

First paragraph: Ebola virus disease (EVD) is a haemorrhagic fever caused by Ebola virus (EBOV) with high infectivity and mortality. EBOV is an enveloped, single-stranded, and negative-sense RNA virus belonging to the Filoviridae family. In contrast to the genus Marburgvirus which contains one single species, the genus Ebolavirus contains 5 species: Zaire ebolavirus (ZEBOV), Sudan ebolavirus (SUDV), Taï Forest ebolavirus (TAFV), Bundibugyo ebolavirus (BDBV) which are pathogenic for humans, and Reston Ebolavirus (RESTV) which infects non human primates. EBOV was first discovered in 1976 in the Democratic Republic of Congo (DRC) and simultaneously in Sudan. Since 1976, EVD has appeared sporadically in DRC, Sudan, Gabon, Uganda, and Congo, with small to large outbreaks and lethality ranging from 50 to 100% with about 2500 cumulative cases until 2013

Diagnostic territorial et gouvernance urbaine de Ziguinchor: une analyse basée sur l'utilisation des TIC, SIG et OSM (Géomatique)

L'amplification démographique de la ville de Ziguinchor suscite l’extension spatiale qui s'accompagne de divers problèmes: dysfonctionnement dans l'aménagement urbain, développement de l'informalité économique et spatiale. Ces problèmes mettent en péril la viabilité économique en créant des déséquilibres entre les besoins croissants en services urbains de la population et les moyens faibles ou limités de la municipalité pour réaliser les investissements nécessaires. Cette situation rend plus alambiquée la gouvernance urbaine. Cet article, adopte un procédé de diagnostic du territoire urbain fondé sur l'analyse spatiale et celle de la territorialité des acteurs, extériorisé sous forme de prototypes spatiaux à travers les mécanismes de la géomatique. Les résultats ont permis d'abord, de faire le diagnostic territorial de la ville de Ziguinchor; ensuite, d'exposer l'essor de l'emploi et l'importance de la géomatique dans la gestion urbaine et enfin, de faire des propositions innovantes permettant l’articulation des pratiques des différents acteurs pour une gouvernance urbaine efficiente.The demographic amplification of the city of Ziguinchor gives rise to spatial extension, which is accompanied by various problems: dysfunction in urban planning, development of economic and spatial informality. These problems jeopardize economic viability by creating imbalances between the growing need for urban services of the population and the weak or limited means of the municipality to make the necessary investments. This situation makes urban governance the most convoluted. This article adopts a method of urban territory diagnosis based on spatial analysis and that of the territoriality of the actors, expressed in the form of spatial prototypes through the mechanisms of geomatics. The results allowed, first, to make the territorial diagnosis of the city of Ziguinchor; then, to expose the growth of employment and the importance of geomatics in urban management and finally, to make innovative proposals allowing the articulation of practices of different actors for efficient urban governance

Quantitative real-time PCR detection of Zika virus and evaluation with field-caught mosquitoes

BACKGROUND Zika virus (ZIKV), a mosquito borne flavivirus is a pathogen affecting humans in Asia and Africa. ZIKV infection diagnosis relies on serology-which is challenging due to cross-reactions with other flaviviruses and/or absence or low titer of IgM and IgG antibodies at early phase of infection- virus isolation, which is labor intensive, time consuming and requires appropriate containment. Therefore, real-time RT-PCR (rRT-PCR) is an appealing option as a rapid, sensitive and specific method for detection of ZIKV in the early stage of infection. So far, only one rRT-PCR assay has been described in the context of the outbreak in Micronesia in 2007. In this study, we described a one step rRT-PCR for ZIKV which can detect a wider genetic diversity of ZIKV isolates from Asia and Africa. RESULTS The NS5 protein coding regions of African ZIKV isolates were sequenced and aligned with representative flaviviruses sequences from GenBank to design primers and probe from conserved regions. The analytical sensitivity of the assay was evaluated to be 32 genome-equivalents and 0.05 plaque forming unit (pfu). The assay was shown to detect 37 ZIKV isolates covering a wide geographic in Africa and Asia over 36 years but none of the 31 other flaviviruses tested showing high analytical specificity. The rRT-PCR could be performed in less than 3 hours. This method was used successfully to detect ZIKV strains from field-caught mosquitoes. CONCLUSION We have developed a rapid, sensitive and specific rRT-PCR for detection of ZIKV. This assay is a useful tool for detection of ZIKV infection in regions where a number of other clinically indistinguishable arboviruses like dengue or chikungunya co-circulate. Further studies are needed to validate this assay in clinical positive samples collected during acute ZIKV infection

Deployment of the Institut Pasteur de Dakar team to Guinea in the Ebola virus Disease outbreak in West-Africa 2014-2016

First paragraph: The unit of Arbovirus and Haemorrhagic Fever Viruses at the Institut Pasteur de Dakar (IPD), a WHO-approved collaborating Centre was the first laboratory deployed to Conakry in the Ebola virus disease (EVD) outbreak in West-Africa. On 20 March 2014, the IPD laboratory received a letter from the WHO and the Guinean Ministry of Health, informing about a suspected haemorrhagic fever outbreak and difficulties to send collected samples to IPD. They therefore requested the deployment of experts to Guinea for technical support in order to diagnose the haemorrhagic fever of unknown origin. The outbreak was identified by the Institut Pasteur (France) on 21 March 2014 [1,2] in samples shipped to France by a Médecins sans Frontières investigation team

Full-genome characterization and genetic evolution of West African isolates of Bagaza virus

Bagaza virus is a mosquito-borne flavivirus, first isolated in 1966 in Central African Republic. It has currently been identified in mosquito pools collected in the field in West and Central Africa. Emergence in wild birds in Europe and serological evidence in encephalitis patients in India raise questions on its genetic evolution and the diversity of isolates circulating in Africa. To better understand genetic diversity and evolution of Bagaza virus, we describe the full-genome characterization of 11 West African isolates, sampled from 1988 to 2014. Parameters such as genetic distances, N-glycosylation patterns, recombination events, selective pressures, and its codon adaptation to human genes are assessed. Our study is noteworthy for the observation of N-glycosylation and recombination in Bagaza virus and provides insight into its Indian origin from the 13th century. Interestingly, evidence of Bagaza virus codon adaptation to human house-keeping genes is also observed to be higher than those of other flaviviruses well known in human infections. Genetic variations on genome of West African Bagaza virus could play an important role in generating diversity and may promote Bagaza virus adaptation to other vertebrates and become an important threat in human health

Changes in the Transmission Dynamic of Chikungunya Virus in Southeastern Senegal.

In Senegal, chikungunya virus (CHIKV) is maintained in a sylvatic cycle and causes sporadic cases or small outbreaks in rural areas. However, little is known about the influence of the environment on its transmission. To address the question, 120 villages were randomly selected in the Kedougou region of southeastern Senegal. In each selected village, 10 persons by randomly selected household were sampled and tested for specific anti-CHIKV IgG antibodies by ELISA. We investigated the association of CHIKV seroprevalence with environmental variables using logistic regression analysis and the spatial correlation of village seroprevalence based on semivariogram analysis. Fifty-four percent (51%-57%) of individuals sampled during the survey tested positive for CHIKV-specific IgG. CHIKV seroprevalence was significantly higher in populations living close to forested areas (Normalized Difference Vegetation Index (NDVI), Odds Ratio (OR) = 1.90 (1.42-2.57)), and was negatively associated with population density (OR = 0.76 (0.69-0.84)). In contrast, in gold mining sites where population density was >400 people per km2, seroprevalence peaked significantly among adults (46% (27%-67%)) compared to all other individuals (20% (12%-31%)). However, traditional gold mining activities significantly modify the transmission dynamic of CHIKV, leading to a potential increase of the risk of human exposition in the region

Detection of Chikunguny a virus by RT-LAMP

Background A single-tube one-step real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of chikungunya virus (CHIKV) targeting the conserved 6K-E1 target region was developed. The assay was validated with sera collected from a CHIKV outbreak in Senegal in 2015. Methodology/Principal findings A novel design approach by combining Principal Component Analysis and phylogenetic analysis of 110 available CHIKV sequences and the LAMP oligonucleotide design software LAVA was used. The assay was evaluated with an External Quality Assessment panel from the European Network for Diagnostics of "Imported" Viral Diseases and was shown to be sensitive and specific and did not cross-detect other arboviruses. The limit of detection as determined by probit analysis, was 163 molecules, and 100% reproducibility in the assays was obtained for 103 molecules (7/8 repetitions were positive for 102 molecules). The assay was validated using 35 RNA samples extracted from sera, and results were compared with those obtained by quantitative RT-PCR carried out at the Institut Pasteur Dakar, demonstrating that the RT-LAMP is 100% sensitive and 80% specific, with a positive predictive value of 97% and negative predictive value of 100%. Conclusions/Significance The RT-LAMP appeared to show superior performance with material stored for months compared to qRT-PCR and can be therefore recommended for use in infrastructures with poor settings

Morbidity associated with sickle cell trait carriers

Background: Sickle cell trait carriers has long considered asymptomatic. This affirmation is now challenged because many patients complain of osteoarticular pain and several organic degenerative complications in particular; renal, eye and sudden death have been described. The objective of this study was to evaluate the morbidity of sickle cell trait and identify risk factors associated.Methods: This is a prospective study with duration of 16 months including 50 patients with sickle cell trait received regular visits (every 6 months) for painful events. Biological assessment was carried out systematically to eliminate rheumatic disease (CRP, ASLO, latex Waler Rose) or metabolic disorders (serum calcium, serum magnesium, and serum uric acid). A correlation between clinical and laboratory data was performed to study the relationship between morbidity observed and biological abnormalities.Results: Mean age of patients was 32 years (12-59) and mean age at diagnosis was 24 years (12-55 years). Sex ratio M/F was 0.16. Clinical symptoms were osteoarticular pain (88%), headache (86%), abdominal pain (76%), muscle cramps (70%), dizziness (56%), biliary lithiasis (6%), femoral head osteonecrosis (2%) and gross haematuria (2%). Seventeen patients (34%) had abnormal metabolic or rheumatic analysis. No risk factor associated with morbidity of patients was identified.Conclusions: This work has allowed us to find that the symptoms presented by sickle cell trait patients are dominated by painful events. This morbidity associated with porting sickle cell trait was not secondary to inflammatory or metabolic disorders or physical activity