Results of the Secov+ project, increased genomic surveillance and data processing capacity of the Italian laboratory network

Improved achievement of quality standards by the network's laboratories, the opening to the sequencing of new infectious agents beyond SARS-CoV-2, such as RSV and influenza, and improved estimates of virus transmissibility thanks to new mathematical models. These are some of the results achieved by the European project "Enhancing whole genome sequencing (WGS), national infrastructures and capacities for COVID-19 and surveillance of other respiratory viruses in Italy" (SeCOV+), whose final meeting was recently held.

Opening the meeting, Paola D'Acapito of the European Health and Digital Executive Agency (HaDEA) noted that 25 countries are involved in the project, with 21 direct funding sources, aimed at establishing a network of sequencing infrastructures or strengthening existing ones. Among the opening remarks was Luca Freschi of the ECDC, who emphasized that effective surveillance of respiratory diseases is a priority for the entire EU. Alessia Mammone of the Ministry of Health's Office 2 - Prevention and Prophylaxis of Communicable Diseases also highlighted the Ministry's contribution to the project, particularly in developing a survey to determine the effectiveness of the project's technical recommendations for the laboratory network and in coordinating periodic surveys.

During the various sessions, the main results achieved over the two years of the project were presented: among these, the evaluation criteria for the sequencing activities carried out by the network were defined, the data management platform was strengthened, sequencing strategies were revised, and an assessment of the laboratories' current capacity to sequence the SARS-CoV-2, influenza, and RSV viruses was conducted. An analysis of the long-term sustainability of the laboratory network was also conducted, and new mathematical models were developed to predict the impact of new variants on the epidemiology of SARS-CoV-2.

"The project has had a significant impact on the network of 70 laboratories in all 21 Italian regions and autonomous provinces," explained Paola Stefanelli, project coordinator. "Genomic surveillance and data analysis capacity has increased, partly through the integration of genomics, epidemiology, and environmental sciences. Furthermore, most of the network's laboratories have achieved the required quality standards."