Introduction of avian metapneumovirus subtype A to the United States: molecular insights and implications

Authors: GORAICHUK, IRYNA - Orise Fellow; TORCHETTI, MIA - Animal And Plant Health Inspection Service (APHIS); KILLIAN, MARY LEA - Animal And Plant Health Inspection Service (APHIS); Kapczynski, Darrell; KULKARNI, ARUN - Georgia Poultry Laboratory Network; SARY, KATHLEEN - Georgia Poultry Laboratory Network; Suarez, David

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/12/2024
Publication Date: 7/5/2024
Citation: Goraichuk, I.V., Torchetti, M., Killian, M., Kapczynski, D.R., Kulkarni, A., Sary, K., Suarez, D.L. 2024. Introduction of avian metapneumovirus subtype A to the United States: molecular insights and implications. Frontiers in Microbiology. 15. https://doi.org/10.3389/fmicb.2024.1428248.
DOI: https://doi.org/10.3389/fmicb.2024.1428248

Interpretive Summary: Avian metapneumovirus (AMPV) is a respiratory viral disease in chickens and turkeys. The virus can be divided into 4 different types, A-D. We considered AMPV to be a foreign animal disease as it not normally found in the United States. In late 2023-early 2024 a new outbreak of APMV-A was identified in several chicken and turkey flocks in several different states. From clinical samples we were able to directly sequence the infected flocks, and we analyzed this sequence data. The virus seen in the United States was closely related to AMPV-A viruses recently reported from Mexico which suggests a cross border introduction. Because the virus is new in the U.S., many labs did not have experience or ability to identify the virus. We reviewed two commercial diagnostic kit and an additional published tests and all three tests appeared to accurately and sensitively identify samples with virus. This virus appears to present an ongoing threat to the U.S. poultry industry.

Technical Abstract: Avian metapneumovirus (aMPV) poses a significant threat to the poultry industry worldwide, primarily affecting turkeys and chickens. The recent detection of aMPV-A and -B subtypes in the United States marks a significant shift after a prolonged period free of aMPV following the successful eradication of the previously circulating subtype C. Hence, the demand for molecular diagnostic tests for aMPV has arisen due to their limited availability in the US market. In this study, we present the molecular characterization based on the complete genome sequence of aMPV subtype A, which was detected in the US for the first time. Four RT-PCR positive samples were subjected to next-generation sequencing analysis, resulting in the assembly of one complete and one near-complete genome sequences. Phylogenetic analysis revealed that the isolated strains clustered within the aMPV-A subtype and were most closely related to recent Mexican strains. A detailed amino acid analysis identified unique mutations in the G gene of the US isolates compared to Mexican strains. Additionally, we compared the performance, cross-reactivity, and limit of detection of our revised aMPV subtype-specific RT-qPCR test with two commercial kits, demonstrating superior detection and subtyping capabilities. These findings highlight the importance of accurate diagnostic methods for disease management in the poultry industry, provide valuable insights into the epidemiology of aMPV, and underscore the need for continued vigilance and surveillance to mitigate its impact on poultry production.