Data and code for "Landscape changes elevate risk of avian influenza virus diversification and emergence in the East Asian-Australasian Flyway"

Highly pathogenic avian influenza viruses (HPAIV) persistently threaten wild waterfowl, domestic poultry, and public health. The East Asian-Australasian Flyway plays a crucial role in HPAIV dynamics due to its large populations of migratory waterfowl and poultry. Over recent decades, this flyway has undergone substantial landscape changes, including both losses and gains of waterfowl habitats. These changes can affect waterfowl distributions, increase contact with poultry, and consequently alter ecological conditions that favor avian influenza virus (AIV) evolution. However, limited research has assessed these likely impacts. Here, we integrated empirical data and an individual-based model to simulate AIV transmission in migratory waterfowl and domestic poultry, including wild-to-poultry spillover and reassortment dynamics in poultry, across landscapes representing the years 2000 and 2015. We used the reassortment incidence as a proxy for ecological and transmission conditions that support viral diversification and the emergence of novel subtypes. Our simulations show that landscape change reshaped the waterfowl distribution, facilitated bird aggregation at improved habitats, increased coinfection, and raised reassortment rate by 1,593%, indicating a substantially higher potential for viral diversification and emergence. Model-generated risk maps show expanded and increased reassortment risk in southeastern China, the Yellow River Basin, and northeastern China. These findings suggest the importance of landscape change as a driver of potential AIV diversification and subtype emergence. This underscores the need for interdisciplinary approaches that integrate landscape dynamics, host movement, and viral evolution to better assess and mitigate future risk.

高致病性禽流感病毒（Highly pathogenic avian influenza viruses, HPAIV）持续对野生水禽、家养家禽以及公共卫生构成威胁。东亚-澳大利西亚迁飞区（East Asian-Australasian Flyway）凭借其庞大的迁徙水禽与家禽种群，在高致病性禽流感病毒的传播动态中发挥着关键作用。近数十年来，该迁飞区的景观发生了显著变化，包括水禽栖息地的缩减与扩增。此类变化可能影响水禽的分布范围，加剧其与家禽的接触，进而改变有利于禽流感病毒（AIV）进化的生态条件。然而，针对此类潜在影响的评估研究仍较为匮乏。本研究整合实证数据与基于个体的模型（individual-based model），模拟了代表2000年与2015年的两类景观场景下，迁徙水禽与家养家禽之间的禽流感病毒传播过程，涵盖野生鸟类向家禽的溢出传播以及家禽体内的病毒基因重配动态。本研究以病毒基因重配发生率作为表征指标，用以衡量支持病毒多样化及新型亚型出现的生态与传播条件。模拟结果表明，景观变化重塑了水禽的分布格局，促使鸟类在优化后的栖息地聚集，提升了混合感染概率，并使病毒重配率提升1593%，这意味着病毒多样化与新型亚型出现的潜力显著增强。模型生成的风险地图显示，中国东南部、黄河流域以及中国东北地区的病毒重配风险范围扩大、强度提升。上述研究结果证实，景观变化是推动禽流感病毒多样化及亚型出现的重要驱动因素。这凸显了整合景观动态、宿主迁徙行为与病毒进化的跨学科研究方法的必要性，以便更好地评估并降低未来的相关风险。