Towards the National Platform for Genomic Surveillance

The PLEpiSeq project is a continuation of the previous project - HERA I, which aimed at creating the bioinformatic platform for genomic-based national epidemiological surveillance in Poland. The platform provides (I) the infrastructure for genomic data storage and computations, (II) tools to support integrations of SARS-CoV-2 genomic sequence data with relevant metadata, (III) algorithms for improving the sequencing representation (algorithms generating random samples), and (IV) pipeline for standardized analysis of raw SARS-CoV-2 sequencing data obtained from laboratories in Poland. With this proposal, we aim to address the molecular epidemiology of other pathogens (i.e. Influenza virus and Salmonella). This will enhance epidemiological surveillance for these diseases in Poland, improve our understanding of how they evolve and spread, allowing for implementation of adequate disease control measures. Successful completion of the project will result in improved links between genomic data and contextual metadata and standardization of laboratory protocols, increase in capacity for advanced bioinformatic analysis and visualization of their results, as well as in building workforce capacity and networking in genomic surveillance. Overall, it will enhance our capacity for outbreak investigation, routine surveillance and responding to future health crises.