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  • 9th January 2023

    CADDE Workshop on Portable Metagenomics for Pathogen Surveillance

    CADDE Workshop on Portable Metagenomics for Pathogen Surveillance – Apply here

    Novel untargeted metagenomic approaches, which detect the total diversity of viruses without a priori knowledge of which viruses are present in a sample, are paving a new era in pandemic prevention and preparedness.

    Our workshop will provide hands-on practical training on the generation and interpretation of portable untargeted metagenomics for real-time virus detection and monitoring. Researchers wanting training in library preparation, portable genome sequencing, analysing and contextualising sequencing data using bioinformatic, phylogenetic and epidemiological tools are welcome to apply.

    Our workshop will be held onsite at the Institute of Tropical Medicine, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil, from the 13 to the 17 March 2023. It is jointly organised by CADDE Team and the MRC Centre for Global Infectious Disease Analysis, and will bring together leading experts involved in sequencing programmes, public health surveillance and epidemiology. A preliminary version of the workshop’s programme can be found here: Preliminary Agenda.

    We will be providing sequencing training using the Oxford Nanopore MinION, a portable hand-held DNA sequencer that can produce >20 Gbases of sequence data in near-real time. Our team of demonstrators and speakers has used this system to track Ebola spread in West Africa, monitor the Zika outbreak across the Americas, investigate the largest yellow fever outbreak in the last 70 years in Brazil, generate thousands of SARS-CoV-2 genomes – including genomes from the first SARS-CoV-2 cases in Latin America in less than 48h and the earliest reports of the Gamma Variant of Concern in Manaus. Our protocols were also used to generate the first mpox genomes in Brazil within 16 hours from sample collection.

    How to Apply

    Places are limited and will be allocated according to the following criteria: applicants must have a background in either biology, public health, bioinformatics and/or wet lab work, and be able to attend all five days of the course. Applications will close on the 27th  January 2023 17:00 BRT.

    The applicants will need to submit a 200 word written statement, a CV and an abstract. We have 40 places for applicants from around the globe.  Registration is free of charge and accommodation arrangements might be available upon request. Successful applicants will be asked to present a poster on their research.

    This workshop has been made possible thanks to funding by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), the Medical Research Council (MRC), the MRC Centre for Global Infectious Disease Analysis, Instituto Todos pela Saúde (ITPS) and the Bill and Melinda Gates Foundation.

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