Prevalence and Genetic Diversity of Zoonotic <i>Leptospira</i> and Hantavirus in Rodents, Lanxi City, 2023–2025

Background: Leptospirosis (caused by Leptospira , a bacterium) and hantavirus disease (caused by hantavirus, a virus) are important zoonoses with rodents as main reservoirs. In this study, we investigated the prevalence and genetic diversity of Leptospira and hantavirus in rodents from rural Lanxi City, Zhejiang Province. Rodents showed a higher Leptospira carriage rate than the national average. All hantavirus isolates were Seoul virus (SEOV) and displayed high genetic divergence from vaccine strains. Notably, a unique local phylogenetic cluster of Leptospira borgpetersenii was identified, indicating potential vaccine mismatch and local evolutionary divergence. Methods: Samples were collected from April 2023 to August 2025, with intensive trapping from April to August annually in 2023–2024 and additional sampling in April 2025. Liver and kidney tissues were collected via aseptic dissection. Real-time fluorescent PCR was used to detect pathogen nucleic acids, and gene sequencing and phylogenetic analysis were performed on positive samples. Results: A total of 350 rodents were captured, with Rattus norvegicus (brown rat) as the dominant species (80.00%). The overall Leptospira carriage rate was 7.14% (25/350), with the highest rate in R. norvegicus (7.86%). The overall hantavirus carriage rate was 1.43% (5/350), distributed mainly in R. norvegicus and Rattus flavipectus (yellow-breasted rat). No coinfection with both pathogens was detected. Genetic analysis identified 12 Leptospira strains as Leptospira interrogans and 2 as L. borgpetersenii ; the latter showed genetic differences from domestic and foreign strains, suggesting a potential evolutionary trend. The two hantavirus strains were both SEOV, closely related to domestic SEOV strains from 2021 but with only 86.08–86.81% nucleotide homology to vaccine strains ( e.g. , 80-39, Z37), indicating natural variation. Conclusions: Rodents in rural Lanxi have a relatively high Leptospira carriage rate, and hantavirus is dominated by the SEOV type. R. norvegicus is the main host of both pathogens. Targeted monitoring and prevention/control measures should be strengthened. Natural genetic variation suggests potential antigenic drift and reduced vaccine matching, which requires further serological validation. Attention should be paid to the impact of pathogen genetic variation on control efforts.