Ebola virus disease has been declared a Public Health Emergency of International Concern in Democratic Republic of the Congo. In the short term, our consortium plans to optimise, manufacture, and validate a novel Ebola rapid diagnostic test (RDT) for deployment at the point of need — that is low cost and high performance. A simple, 5 minute, high performance test, that complements complex laboratory tools, is urgently needed to ensure earliest possible detection of Ebola in the heart of communities experiencing an outbreak. Successful deployment will lead to an optimised and evaluated device for manufacture to support the current outbreak in DRC, surveillance in neighbouring regions, and in time post-DRC outbreak surveillance. In the long term, we envision substantial impact generated by establishing a new model for sustainable delivery of high performance outbreak diagnostics, deployed at the point of need. Accordingly, diaTropix - a new manufacturing facility dedicated to epidemics and neglected diseases in Dakar, Senegal - will be set up with the capability, expertise, and reagents to produce rapid diagnostics responsively to evolving outbreaks — with Ebola demonstrating proof of concept and feasibility, and a portfolio of rapid diagnostics in the pipeline for dengue, yellow fever, measles, and malaria.

ZIKAlliance is a multidisciplinary project with a global "One Health" approach, built: on a multi-centric network of clinical cohorts in the Caribbean, Central & South America; research sites in countries where the virus has been or is currently circulating (Africa, Asia, Polynesia) or at risk for emergence (Reunion Island); a strong network of European and Brazilian clinical & basic research institutions; and multiple interfaces with other scientific and public health programmes. ZIKAlliance will addrees three key objectives relating to (i) impact of Zika virus (ZIKV) infection during pregnancy and short & medium term effects on newborns, (ii) associated natural history of ZIKV infection in humans and their environment in the context of other circulating arboviruses and (iii) building the overall capacity for preparedness research for future epidemic threats in Latin America & the Caribbean. The project will take advantage of large standardised clinical cohorts of pregnant women and febrile patients in regions of Latin America and the Caribbean were the virus is circulating, expanding a preexisting network established by the IDAMS EU project. I will also benefit of a very strong expertise in basic and environmental sciences, with access to both field work and sophisticated technological infrastructures to characterise virus replication and physiopathology mechanisms. To meet its 3 key objectives, the scientific project has been organised in 9 work packages, with WP2/3 dedicated to clinical research (cohorts, clinical biology, epidemiology & modeling), WP3/4 to basic research (virology & antivirals, pathophysiology & animal models), WP5/6 to environmental research (animal reservoirs, vectors & vector control) , WP7/8 to social sciences & communication, and WP9 to management. The broad consortium set-up allow gathering the necessary expertise for an actual interdisciplinary approach, and operating in a range of countries with contrasting ZIKV epidemiological status.

In the perspective of increasing the scientific and technological improvement of West Africa, the Institut Pasteur de Dakar (IPD) is strengthening its sequencing platform dedicated to study African diseases targeting the principal genetic factors contributing to infectious disease emergence from the pathogen, the host, the reservoir and the vector. In this regard, IPD is willing to acquire the NovaSeq 6000 System (Illumina) to reach large amounts of data analysis such as host, reservoir, and vector whole-genome sequencing (WGS) as well as ultradeep exome sequencing. An optimized workflow will allow multiplexing samples and reducing the amount of DNA input. The NovaSeq 6000 System also possesses a fully automated onboard cluster generation for reducing hands-on time. The NovaSeq 6000 System is compatible with various Illumina library preparation kits already in use at IPD and linked to the data science group making it an ideal long-term investment. The NovaSeq 6000 System will be positioned and maintained in IPD Sequencing Platform, which is located in a BSLII virology laboratory, fully accessible for all IPD scientists. In addition, through collaborations and training, the NovaSeq 6000 System will be available for researchers outside of IPD. A dedicated and experienced young staff scientist will operate the system. The Institut Pasteur de Dakar is a Senegalese Foundation of public utility under the patronage of the Ministry of Health and Institut Pasteur in Paris to meet the challenges of the future in the biomedical scientific research, public health, education and vaccine production. Our research is focused on high importance infectious diseases in West Africa such as arboviruses (Dengue, Zika), influenza, rabies and recently COVID-19, multi drug resistant pathogenes (tuberculosis), malaria. With this grant application, we request a NovaSeq 6000 System (Illumina) to reach large amounts of data analysis such as host, reservoir, and vector whole-genome sequencing (WGS), ultradeep exome sequencing to advance our research projects in a low-middle income country.It is indispensable for projects to understand (i) the genetic contribution of viruses to a disease outbreak, (ii) the transmission chains, (iii) drug resistance emergence, (iv) genetic diversity dynamic, (v) human/reservoir/vector viral quasi-specie dynamic, (vi) malaria genetic driven drug resistance.