Tawidian Patil, Torchetti Mia K, Killian Mary L, Lantz Kristina, Dilione Krista E, Ringenberg Jourdan M, Bevins Sarah N, Lenoch Julianna B, Ip Hon S
U.S. Geological Survey, National Wildlife Health Center Madison, Madison, WI 53711, USA.
Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA.
Viruses. 2024 Nov 22;16(12):1818. doi: 10.3390/v16121818.
The introduction of HPAI H5N1 clade 2.3.4.4b viruses to North America in late 2021 resulted in avian influenza outbreaks in poultry, mortality events in many wild bird species, and spillovers into many mammalian species. Reassortment events with North American low-pathogenic virus were identified as early as February 2022 and over 100 genotypes have been characterized. Such diversity increases the complexity and time required for monitoring virus evolution. Here, we performed ordination and clustering analyses on sequence data from H5N1 viruses identified in North America between January 2020 and December 2023 to visualize the genotypic diversity of viruses in poultry and wildlife populations. Our results reveal that ordination- and cluster-based approaches can complement traditional phylogenetic analyses specifically for the preliminary assignment of H5N1 viruses to genotypic groups or to identify novel genotypes. Our study expands current knowledge on the genotypic diversity of H5N1 viruses in North America and describes a rapid approach for early virus genotype assignment.
2021年末，高致病性禽流感H5N1 2.3.4.4b分支病毒传入北美，导致家禽爆发禽流感，许多野生鸟类物种出现死亡事件，并传播到许多哺乳动物物种。早在2022年2月就发现了与北美低致病性病毒的重配事件，已鉴定出100多种基因型。这种多样性增加了监测病毒进化的复杂性和所需时间。在此，我们对2020年1月至2023年12月在北美鉴定出的H5N1病毒的序列数据进行了排序和聚类分析，以可视化家禽和野生动物种群中病毒的基因型多样性。我们的结果表明，基于排序和聚类的方法可以补充传统的系统发育分析，特别是用于将H5N1病毒初步分配到基因型组或识别新基因型。我们的研究扩展了当前对北美H5N1病毒基因型多样性的认识，并描述了一种早期病毒基因型分配的快速方法。
