Detection and genome sequence analysis of avian metapneumovirus subtype A viruses circulating in commercial chicken flocks in Mexico

Authors: KARIITHI, HENRY - Orise Fellow; CHRISTY, NANCY - Boehringer Ingelheim; DECANINI, EDUARDO - Boehringer Ingelheim; LEMIERE, STEPHANE - Boehringer Ingelheim; VOLKENING, JEREMY - Base2bio; AFONSO, CLAUDIO - Base2bio; Suarez, David

Submitted to: Veterinary Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/17/2022
Publication Date: 10/19/2022
Citation: Kariithi, H.M., Christy, N., Decanini, E.L., Lemiere, S., Volkening, J.D., Afonso, C.L., Suarez, D.L. 2022. Detection and genome sequence analysis of avian metapneumovirus subtype A viruses circulating in commercial chicken flocks in Mexico. Veterinary Sciences. 9(10):579. https://doi.org/10.3390/vetsci9100579.
DOI: https://doi.org/10.3390/vetsci9100579

Interpretive Summary: The use of Next Generation Sequencing (NGS) techniques continue to identify pathogens in clinical samples continues to improve. Often full length viral genomes can be identified in samples and this sequence information can be used to not only identify what pathogens are in samples, but also determine the genotype, pathotype, or lineage of a virus. This information can be used to predict which viruses are likely to cause severe disease and can help guide the use of what vaccines should be used for control efforts. As part of a project to improve NGS for diagnostics, samples were collected from poultry farms in Mexico. One of the most common pathogens identified was avian metapneumovirus subtype A (AmPV-A), which is an important respiratory disease viral pathogen in chickens. The full genomes of over 11 viruses were identified and analyzed. Avian metapneumovirus has four different subtypes, A-D, and the subtype A viruses have been previously been found in Mexico, but this is the first time the complete genomes of the Mexican AmPV-A viruses have been reported and compared to other available sequences. that require targeted vaccination for full protection. Five different genotypes were identified which provides a much clearer picture of viruses circulating in Mexico. Because AmPV-A is not found in the United States, a modified real-time RT-PCR test was evaluated that can quickly identify the virus from poultry samples.

Technical Abstract: Avian metapneumoviruses (aMPV subtypes A-D) are respiratory and reproductive pathogens of poultry. Since aMPV-A was initially reported in Mexico in 2014, there have been no additional reports of its detection in the country. Using nontargeted next-generation sequencing (NGS) of FTA card-spotted respiratory samples from commercial chickens in Mexico, seven full genome sequences of aMPV-A (lengths of 13,288–13,381 nucleotides) were de novo assembled. Additionally, complete coding sequences of genes N (n = 2), P and M (n = 7 each), F and L (n = 1 each), M2 (n = 6), SH (n = 5) and G (n = 2) were reference-based assembled from another seven samples. The Mexican isolates phylogenetically group with, but in a distinct clade separate from, other aMPV-A strains. The genome and G-gene nt sequences of the Mexican aMPVs are closest to strain UK/8544/06 (97.22–97.47% and 95.07–95.83%, respectively). Various amino acid variations distinguish the Mexican isolates from each other, and other aMPV-A strains, most of which are in the G (n = 38), F (n = 12), and L (n = 19) proteins. Using our sequence data and publicly available aMPV-A data, we revised a previously published rRT-PCR test, which resulted in different cycling and amplification conditions for aMPV-A to make it more compatible with other commonly used rRT-PCR diagnostic cycling conditions. This is the first comprehensive sequence analysis of aMPVs in Mexico and demonstrates the value of nontargeted NGS to identify pathogens where targeted virus surveillance is likely not routinely performed.