Integrated Genomic and Epidemiological Surveillance to Monitor SARS‐CoV‐2 Variants in Italy: Insights From the JN.1 Case Study (2023–2024)

: The epidemiology of SARS-CoV-2 is marked by the continuous emergence of new lineages. Early detection and assessment of their transmissibility can be challenging for surveillance systems that rely solely on case time series data. Genomic surveillance, focusing on identifying and characterizing circulating variants, can provide early insights into their epidemiological impact. Phylogenetic and phylodynamic methods were applied to sequence data collected between October 2023 and January 2024 to study the transmission of the JN.1 variant in Italy. The genomic surveillance encompassed two data flows: flash surveys estimating variant prevalence and continuous sampling to identify emerging variants. We estimated the effective reproduction number (Re) of JN.1 using a phylodynamic birth-death model. Results were compared with the daily net reproduction number (Rt) of SARS-CoV-2 estimated from time series of hospital admissions recorded through epidemiological surveillance. We traced back the appearance of JN.1 in Italy to October 2023, with subvariants emerging and co-circulating shortly thereafter. JN.1 became dominant nationwide by the end of 2023. According to phylodynamic analysis, the Re of JN.1 was 1.73 (95% CI: 1.36-2.28) in mid-November, and its transmissibility declined over the following months. This trend aligned with Rt estimates from epidemiological surveillance, encompassing all co-circulating lineages. The high transmissibility of JN.1 anticipated the rise in its prevalence in the population and showed a temporal correlation with a transient increase in COVID-19 hospitalizations. Integrating genomic and epidemiological surveillance enhances pathogen monitoring and the assessment of new lineages' transmissibility, providing complementary evidence to patterns observed through standard surveillance.