Abstract
During the COVID-19 pandemic, detection of Sars-CoV-2 in wastewater has reinforced the strength of wastewater-based epidemiology to monitor outbreaks and to deliver complementary data to guide and evaluate socio-economic policy strategies. Wastewater indeed contains a wealth of information on types of pathogens circulating in humans. This unique virome and microbiome window has not yet been sufficiently exploited for its many benefits. With advances in molecular methods available today, we can map the virome and antimicrobial resistance genes of populations through wastewater surveillance, and optimize monitoring of the next global challenges linked to pathogens. Optimization of methods for wastewater collection, for pre-treatment of wastewater and for nucleic acid purification will be optimized during this Phd for a selection of pathogens, including SARS-CoV-2 and other respiratory viruses. In addition, detection methods will be developed for other pathogens such as Adenoviruses, Enteroviruses, Hepatitis E virus and Norovirus, and for a selection of AMR genes. Finally, sampling and wastewater processing methods will be optimized for use in rural and low resource settings.
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