SeaWater&FreshWater Raw sequence reads
This study aimed to explore the presence and phylogenetics of IAV in freshwater and seawater samples from eastern China, utilizing metatranscriptomic and metagenomic sequencing. Our findings revealed that IAV fragments in seawater shared a high degree of homology with human H3N2 strains circulating in North America over the past three years, while those in freshwater were similar to historical avian strains from neighboring countries. Our analyses demonstrated strong correlations between IAV and various microbial taxa, including specific bacteria and fungi, suggesting that these microorganisms may facilitate viral persistence and transmission. Interaction network analyses highlighted complex relationships, indicating that environmental microbes could play a critical role in shaping IAV dynamics. Notably, IAV was more frequently detected in freshwater environments that also harbored Uroviricota, suggesting a potential role for these viruses in IAV transmission. These findings emphasized the importance of monitoring IAV in aquatic ecosystems, particularly those inhabited by migratory waterfowl, to mitigate public health risks associated with zoonotic transmission. Our research provided new insights into the ecological interactions influencing IAV epidemiology, underscoring the need for integrated surveillance strategies to anticipate future viral outbreaks.