Mapping the genetic diversity of avian metapneumovirus circulating among GA poultry flocks

Authors: Alvarez Narvaez, Sonsiray; SARY, KATHLEEN - Georgia Poultry Laboratory Network; Goraichuk, Iryna; KULKARNI, ARUN - Georgia Poultry Laboratory Network; Kapczynski, Darrell; Suarez, David

Submitted to: Avian Diseases
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/16/2025
Publication Date: 2/4/2026
Citation: Alvarez Narvaez, S., Sary, K., Goraichuk, I., Kulkarni, A., Kapczynski, D.R., Suarez, D.L. 2026. Mapping the genetic diversity of avian metapneumovirus circulating among GA poultry flocks. Avian Diseases. Volume 69, Issue S1.

Interpretive Summary: Avian metapneumovirus is a highly contagious respiratory viral infection of chickens and turkeys. The virus had been eliminated from U.S. poultry, but in late 2023 two variants of the virus, subtypes A and B, were introduced into the U.S. and spread rapidly throughout the poultry industry causing sizable economic losses because of the disease. The rapid spread of the virus was surprising because farms already had enhanced biosecurity measures because of avian influenza virus. To try and understand how the virus was spreading so rapidly, a research study evaluated virus found on farms in Georgia. The viruses were sequenced and compared to see how closely the viruses were from each outbreak farm. A total of 43 viruses were sequenced which showed that related viruses were found more often in the same company as compared to viruses from different companies in close proximity. This provides some ideas on how the virus could be spreading with common source factors that can potentially be mitigated. This is the first time that full genome sequencing has been used for avian metapneumovirus epidemiological analysis.

Technical Abstract: 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 (U.S.), which was considered an aMPV-free country for poultry since the eradication of the last cases of aMPV-C in the early 2000’s. Unfortunately, aMPV subtypes A and B were both introduced into the U.S. in 2023-24, with outbreaks reported in many states. The rapid spread of aMPV 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 stains circulating in the US, 68 RT-qPCR positive oropharyngeal swabs collected between February and June 2024 from 36 chicken farms belonging to 17 poultry production companies across the state of Georgia (GA), U.S. were subjected to next-generation sequencing analysis. 43 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 American aMPV-B viruses The combination of a phylogenetic analysis and the available metadata revealed genetic clustering by production company, and also 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 several viral introduction events into GA, likely from another U.S. source. Overall, this work helps characterize aMPV-B strains circulating in GA and genetic connections that will inform the affected companies to adapt their biosafety measures for aMPV containment.