Tracking the Virus Spread and Evolution of Emerging Avian Metapneumovirus Subtypes A and B in U.S. Poultry

Avian metapneumovirus (aMPV) is a highly contagious respiratory pathogen that affects poultry. The main subtypes of aMPV are A, B, C, and D. Until recent outbreaks, only subtype C had been detected in the United States. However, since their initial detection in early 2024, subtypes A and B have rapidly spread across various poultry types. This study was conducted using clinical samples submitted to the Animal Disease Research Diagnostic Laboratory at South Dakota State University following the emergence of aMPV subtypes A and B in the U.S. poultry industry. The samples, collected from January to August 2024, were analyzed to assess the extent of spread and to examine associations with factors such as geographic location, age, species, and sample type of these emerging viruses. A total of 1487 samples from 975 turkey and chicken farms in 17 states were tested. Of these, 489 tested positive for either subtype A or B, with the majority testing positive for subtype B. Kentucky, North California, Pennsylvania, South Carolina, and Virginia tested positive for subtype B. In contrast, Arkansas, California, Minnesota, Missouri, North Dakota, and South Dakota tested positive for both subtypes A and B. Most positive samples came from birds aged 0-5 wk, followed by those aged 6-10 wk, with the highest proportion from commercial turkey farms. Entire genomes of nine aMPV-A strains and six aMPV-B strains from different turkey and chicken farms across various states were assembled. Analysis of these genomes revealed genomic diversity from the previously detected strains worldwide. Despite this, the U.S.-detected subtypes A and B shared more than 99% similarity at both the whole-genome and G gene levels. Although unique amino acid mutations have been detected in both A and B sequences. The subtype A strains detected in the fall of 2024 from Minnesota and South Dakota showed a single amino acid substitution asparagine to aspartic acid at position 263 (N263D). The three Alabama (AL) strains sequenced in 2025 had a new substitution of serine to aspartic acid at position 171 (S171D), while the AL/5614 strain had an additional threonine to methionine at position 269 (T269M) mutation. In conclusion, this study highlights the rapid spread of subtypes A and B among U.S. poultry. Based on the detected subtypes A and B in this study and other strains available in GenBank, new variants (monophyletic groups) have emerged in the United States, showing high genomic identity even after a year of circulation in poultry populations and minimal mutations.