Report of the existing surveillance and development needs in TZ, DRC, BF
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Report of the existing infectious disease surveillance and development needs including potential of environmental surveillance actions in TZ, DRC, and BF.
Data generation processes integration
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Report on integration with data generation processes, allowing data collection and submission from local data generators to a central data management system for integration.
Minutes of Annual Progress and SAB meetings
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First meeting M13Second meeting M25Third meeting M36The minutes detail the agenda, participants, date, questions, as well as conclusions or decisions from the meetings.
Educational program review
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Review of current existing material for education within bioinformatics and sequencing
Publications
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Peer reviewed papers, newsletters and policy briefsFirst: M12Second: M24Third: M36
Dissemination and exploitation plan
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Local data processing
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Report on established local data processing and QC analysis to ensure data quality and efficient use of samples.
Webinar records describing processing pathways as training video. Laboratory handbook (SOPs) for mobile surveillance workflow transferred to Zenodo
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Laboratory handbook that will contain standard operating procedures (SOPs) for mobile surveillance workflow will be published on Zenodo webpage (https://zenodo.org/). The laboratory handbook will include sampling methodology, selected DNA/RNA extraction methods and procedures on quantitative (qPCRs) and qualitative analysis (Oxford Nanopore sequencing). In the last phase of the project duration a final version of Laboratory handbook with updated SOPs protocols will be published. The same SOPs will be used as the basic for the preparation of webinars being published on the Cordis website or YouTube.
Sample pre-treatment SOP
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Laboratory handbook (SOPs) for environmental surveillance in sub-Saharan countries. Pre-treatment of environmental samples, microbiological and molecular detection, quantification, and high-throughput sequence-based characterization.
Kick-off meeting report
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A detailed summary with agenda, participants, and conclusions/objectives /follow-ups from the initial meeting.
Yearly status update on collaboration activities
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Yearly status update on collaboration activities (12, 24, 36).
Environmental pathogen surveillance protocol in sub-Saharan countries
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Report entailing the protocol proposal for environmental pathogen surveillance of selected infectious diseases in sub-Saharan countries.
Signing of a Collaboration Agreement
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The collaboration within the Genomic Epidemiology Network will be governed by a Collaboration Agreement and membership will include all participating projects that are linked through Article 7 in their grant agreements, namely EpiGen Ethiopia, GenPath Africa, GREAT-LIFE, PANGenS, ODIN, NGS4PublicHealth.
