Geographic Variability of Severe Fever with Thrombocytopenia Syndrome Virus Genomes in Miyazaki Prefecture, Japan: A Cross-sectional Molecular Epidemiological Study

Background Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne disease caused by the SFTS virus (SFTSV). In Japan, the highest number of SFTS cases has been reported in Miyazaki Prefecture. Despite previous genomic studies, the regional genomic diversity of SFTSV in Japan has not been completely characterized at the regional level. Hence, in this study, we aimed to analyze the whole genome sequencing of SFTSV strains collected in Miyazaki Prefecture to assess their genomic diversity. Methods Epidemiological data from patients were analyzed, and amplicon-based whole genome sequencing of SFTSV was performed using serum or plasma samples collected between 2012 and 2023 in Miyazaki Prefecture. The resulting sequences were used to construct a phylogenetic tree, and the distribution of SFTSV genotypes was analyzed according to the presumed regions of infection. Results The phylogenetic analysis revealed that four genotypes of SFTSV, including currently unclassifiable genotypes and a novel genotype named J4, were present in Miyazaki Prefecture. Analysis of the geographic distribution of each genotype revealed an association between the genotypes and presumed regions of infection. Further, genetic reassortment and recombination were confirmed in Japanese strains. Conclusions This study provides the largest whole‑genome analysis of SFTSV conducted in Japan to date, and confirmed that the genotypes of SFTSV in Miyazaki Prefecture exhibited strong regionality. The results suggested limited dispersion of SFTSV through ticks and wild animals. However, the presence of genetic recombination indicated that SFTSV may have been dispersed to distant regions by birds. SFTSV genome analysis may help estimate infection locations, particularly for cases with an unclear exposure history.