Enhancing Whole Genome Sequencing (WGS), national infrastructures and capacities to respond to the Covid-19 pandemic in Italy

Despite a reduction in the number of clinical severe cases of COVID-19, SARS-CoV-2 circulation increased, driven by waning vaccine effectiveness, novel viral variants and the progressive relaxation of non-pharmaceutical interventions. The possibility of a genetic drift of SARS-CoV-2 towards novel prevalent variants with uncertain consequences on the epidemiology and clinical presentation of COVID-19 exists. In Italy, genomic surveillance of SARS-CoV-2 is performed through periodic prevalence surveys, continuous sequencing in specific target-groups and periodic sequencing of raw sewage samples. While specific national funding has been established for some sequencing activities, the sustainability of periodic prevalence surveys is still uncertain. In addition, the completeness, timeliness and quality of the sequences uploaded to the national genomic surveillance platform Italian COVID-19 Genomic (I-Co-Gen) have margins of improvement and the reports produced currently do not integrate data from different SARS-CoV-2 surveillance flows in a common analysis. The project aims to: 1. Support the ongoing enhancement of the Whole Genome Sequencing capacity of the laboratories within the Italian genomic laboratory network and the periodic conduction of prevalence surveys, 2. Support the consolidation and quality of centralized genomic data collection and the establishment of innovative integrated data analysis of genomic and epidemiological data. In this view, the project will significantly contribute to strengthen laboratory preparedness and response, build capacity on genomic surveillance and innovate data analysis through the integration of human genomic, epidemiological and environmental sectors, also using statistical and mathematical models. The project will be coordinated by the Istituto Superiore di Sanità as national competent authority, and will involve both the Ministero della Salute and the Fondazione Bruno Kessler for their respective specific expertise.