Genetic Diversity of Recent U.S. Avian Metapneumovirus Subtype B Viruses Suggests Separate Incursions into Commercial Poultry Flocks

Avian metapneumovirus (aMPV) is an important global respiratory pathogen for poultry, primarily affecting turkeys and chickens. Until recently, subtype C was the only aMPV ever detected in the United States, which was considered an aMPV-free country for poultry since the eradication of the last cases of aMPV-C in the early 2000s. However, aMPV subtypes A and B were both detected in the United States in 2023-2024, with outbreaks reported in many states. The rapid spread of aMPVs in poultry, despite increased biosecurity practices driven by the avian influenza threat, highlights a gap in our epidemiological knowledge regarding these viruses, making effective preventative measures difficult to establish. To improve our understanding of the genetic characteristics and the transmission of aMPV strains circulating in the United States, 43 RT-qPCR-positive oropharyngeal swabs collected between February and June 2024 from 32 chicken farms belonging to 18 poultry production companies across the state of Georgia were subjected to next-generation sequencing analysis. Forty-two complete or nearly complete aMPV genomes were obtained from the sequencing data, all identified as subtype B, and sharing high genetic similarity among themselves and to other recent North and South American aMPV-B viruses. The combination of phylogenetic analysis and the available metadata revealed genetic clustering by production company and by proximity between farms. Additionally, a comprehensive single-nucleotide polymorphism (SNP) analysis showed the maximum genetic divergence (45 SNPs) between aMPVs from different companies, suggesting multiple viral introduction events into Georgia, likely from other U.S. sources. Overall this work helps characterize aMPV-B strains circulating in the United States and genetic connections that will inform the affected companies to adapt their biosafety measures for aMPV containment.