Background: No studies have deeply examined the phylogenetic patterns and spatiotemporal spread of H1N1pdm09 in Anhui Province, China.

Methods: We conducted a genome-wide analysis of 162 historical epidemic strains in Anhui Province, China to understand the phylogenetic relationships and geographic clustering, incoming and outgoing events, and evolutionary dynamics of the strains.

Results: The number of strains available for sequencing was higher for the period 2018-2023, reflecting intensified surveillance activity. Time of most recent common ancestor (TMRCA) estimates for major clades in Anhui were generally delayed compared to global estimates, suggesting Anhui province often acted as a recipient in the global diffusion network. The neuraminidase (NA) fragments had higher dN/dS values than the hemagglutinin (HA) fragments. The circulation pattern of the strain in Anhui Province, China was mainly from central to northern, followed by northern to central and central to southern. Central Anhui appeared as a hub in the inferred provincial spread pattern of H1N1pdm09 in Anhui Province, China. Calculation of transmission events for the whole country showed that the main source of the epidemic strain in Anhui Province was East China. Notably, during the 2023 nationwide uptick, Anhui Province appeared to be a significant source contributing to sporadic cases in other regions.

Conclusion: The above results offer a scientific blueprint for enhancing provincial genomic surveillance systems, facilitating the early detection of emerging variants, as well as emphasize the importance of central Anhui in regional spread, though parallel introductions from other regions cannot be excluded.