Respiratory Syncytial Virus (RSV) in an Italian Pediatric Cohort: Genomic Analysis and Circulation Pattern in the Season 2022–2023

There is growing interest in the molecular surveillance of the respiratory syncytial virus (RSV) and data concerning the virus molecular epidemiology in high-risk pediatric patients in Italy are still limited. A total of 127 RSV-positive swabs collected in 2022-2023 season were analyzed. Whole genomes were obtained by next-generation sequencing and used for phylogenetic and phylodynamic analyses. A large proportion of the subjects had required hospitalization (78%) and age of hospitalized subjects was significantly lower than that of nonhospitalized (69 vs. 129 days; p < 0.0001). Genomic analysis suggested a significant increase in nucleotide variability in recent samples compared to previous waves and especially in subtype A. Phylogenetic analysis identified 14 and 16 clades including Italian strains in RSV-A and B, respectively. Italian strains tended to group together forming monophyletic groups, 9 in RSV-A and 13 in RSV-B, probably representing local chains of transmission. A few of those pure Italian subclades began in 21-22 wave and persisted for more than 1 year. For both subtypes the skyline plot showed two peaks in transmissions, the first between 2017 and 2019, followed by a temporary reduction in 2021 coinciding with the widespread use of control measures against COVID-19 and the second at the beginning of 2023. Accordingly, the Re estimates showed fluctuating values. This study suggests that the large circulation of RSV following pandemic restrictions is partly due to the introduction of viral strains already circulating across Europe, and partly to strains that persist in our region from one season to the next.