France went through three deadly epidemic waves due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing major public health and socioeconomic issues. We proposed to study the course of the pandemic along 2020 from the outlook of two major Parisian hospitals earliest involved in the fight against COVID-19. Genome sequencing and phylogenetic analysis were performed on samples from patients and health care workers (HCWs) from Bichat (BCB) and Pitié-Salpêtrière (PSL) hospitals. A tree-based phylogenetic clustering method and epidemiological data were used to investigate suspected nosocomial transmission clusters. Clades 20A, 20B and 20C were prevalent during the spring wave and, following summer, clades 20A.EU2 and 20E.EU1 emerged and took over. Phylogenetic clustering identified 57 potential transmission clusters. Epidemiological connections between participants were found for 17 of these, with a higher proportion of HCWs. The joint presence of HCWs and patients suggest viral contaminations between these two groups. We provide an enhanced overview of SARS-CoV-2 phylogenetic changes over 2020 in the Paris area, one of the regions with highest incidence in France. Despite the low genetic diversity displayed by the SARS-CoV-2, we showed that phylogenetic analysis, along with comprehensive epidemiological data, helps to identify and investigate healthcare associated clusters.
【저자키워드】 SARS-CoV-2, viral infection, Epidemiology, viral epidemiology, viral evolution, Next-generation sequencing, Phylogeny, 【초록키워드】 COVID-19, public health, coronavirus, pandemic, Health care, hospital, health care workers, nosocomial, Sequencing, severe acute respiratory syndrome Coronavirus, hospitals, Genome sequencing, Phylogenetic analysis, Region, Contamination, Viral, HCWs, healthcare, Patient, Clustering, Clusters, Nosocomial transmission, France, Health care worker, clade, clades, genetic diversity, epidemiological data, incidence, respiratory, summer, change, epidemic waves, Phylogenetic, HCW, epidemic wave, connection, acute respiratory syndrome, two groups, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, Paris, help, participant, transmission clusters, potential transmission, prevalent, joint, Course, highest, identify, performed, involved, proportion, were used, the SARS-CoV-2, 【제목키워드】 hospital, SARS-CoV-2 genome, Lineage, Cluster, Paris, characterized,