Towards real-time monitoring of COVID-19 nosocomial clusters using SARS-CoV-2 genomes in a university hospital of the French Alps

Abstract

Objectives: Experience of Nextstrain [1,2] and its approach adapted to the local context encouraged us to carry out real-time monitoring of COVID-19 nosocomial clusters in our establishment, the Grenoble Alpes University Hospital.

Patients and methods, results: Through identification from electronic health records of nosocomial pathways and clusters and calculation of genetic distances from sequenced samples of COVID-19 patients, we were able to identify potential nosocomial clusters in very close to real time with a significant time saving compared to classical epidemiological surveillance, and to better understand and characterize nosocomial clusters.

Conclusion: Through early detection and characterization of clusters, we may prevent infection of our patients by further implementing the appropriate measures.

Keywords: COVID-19; Clusters; Monitoring; Nosocomial; Phylogenetics.