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Geographical Expansion of Avian Metapneumovirus Subtype B: First Detection and Molecular Characterization of Avian
Muhammad Luqman1, Naveen Duhan1, Gun Temeeyasen1
1Animal Disease Research and Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, College of Agriculture, Food & Environmental Sciences, South Dakota State University, Brookings, SD 57007, USA.
Abstract:
Avian metapneumovirus (aMPV), classified within the Pneumoviridae family, wreaks havoc on poultry health. It typically causes upper respiratory tract and reproductive tract infections, mainly in turkeys, chickens, and ducks. Four subtypes of AMPV (A, B, C, D) and two unclassified subtypes have been identified, of which subtypes A and B are widely distributed across the world. In January 2024, an outbreak of severe respiratory disease occurred on turkey and chicken farms across different states in the US. Metagenomics sequencing of selected tissue and swab samples confirmed the presence of aMPV subtype B. Subsequently, all samples were screened using an aMPV subtype A and B multiplex real-time RT-PCR kit. Of the 221 farms, 124 (56%) were found to be positive for aMPV-B. All samples were negative for subtype A. Six whole genomes were assembled, five from turkeys and one from chickens; all six assembled genomes showed 99.29 to 99.98% nucleotide identity, indicating a clonal expansion event for aMPV-B within the country. In addition, all six sequences showed 97.74 to 98.58% nucleotide identity with previously reported subtype B sequences, e.g., VCO3/60616, Hungary/657/4, and BR/1890/E1/19. In comparison to these two reference strains, the study sequences showed unique 49-62 amino acid changes across the genome, with maximum changes in glycoprotein (G). One unique AA change from T (Threonine) to I (Isoleucine) at position 153 in G protein was reported only in the chicken aMPV sequence, which differentiated it from turkey sequences. The twelve unique AA changes along with change in polarity of the G protein may indicate that these unique changes played a role in the adaptation of this virus in the US poultry. This is the first documented report of aMPV subtype B in US poultry, highlighting the need for further investigations into its genotypic characterization, pathogenesis, and evolutionary dynamics.
Insights
Avian metapneumovirus subtype B caused a severe respiratory disease outbreak in US poultry in 2024. Genetic analysis revealed clonal expansion and unique changes, suggesting viral adaptation in domestic birds.
Area of Science:
- Veterinary Virology
- Poultry Health
- Molecular Epidemiology
Background:
- Avian metapneumovirus (aMPV) within the Pneumoviridae family causes significant respiratory and reproductive issues in poultry worldwide.
- Subtypes A and B of aMPV are globally prevalent, impacting turkeys, chickens, and ducks.
- The emergence of novel viral strains poses a continuous threat to avian populations.
Purpose of the Study:
- To identify and characterize the causative agent of a severe respiratory disease outbreak in US poultry in January 2024.
- To determine the genetic makeup and evolutionary dynamics of the circulating aMPV strain.
- To establish the first documented report of aMPV subtype B in US poultry.
Main Methods:
- Metagenomics sequencing was employed to detect aMPV in affected tissue and swab samples.
- A multiplex real-time RT-PCR assay was utilized to screen 221 farms for aMPV subtypes A and B.
- Whole genome sequencing and comparative analysis were performed on positive samples to assess genetic relatedness and identify unique mutations.
Main Results:
- Avian metapneumovirus subtype B was confirmed as the cause of the outbreak, affecting 56% (124/221) of surveyed farms; subtype A was not detected.
- Whole genome sequencing of six isolates (five turkey, one chicken) revealed high nucleotide identity (99.29-99.98%), indicating clonal expansion of aMPV-B in the US.
- The US aMPV-B sequences exhibited unique amino acid changes (49-62 across the genome, particularly in the G protein) compared to global reference strains, suggesting viral adaptation.
Conclusions:
- This study reports the first detection of avian metapneumovirus subtype B in US poultry, associated with a significant respiratory disease outbreak.
- The genetic homogeneity and unique mutations observed in the US isolates suggest recent introduction and rapid clonal expansion, potentially driven by adaptation.
- Further research into the pathogenesis, genotypic characteristics, and evolutionary trajectory of this aMPV-B strain is crucial for effective disease management in poultry.
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