Rapid evolution of Mexican H7N3 highly pathogenic avian influenza viruses in poultry

Authors: YOUK, SUNG-SU - Orise Fellow; LEE, DONG-HUN - University Of Connecticut; FERREIRA, HELENA - Orise Fellow; Afonso, Claudio; ABSALON, ANGEL - Vaxbiotek Sc; Swayne, David; Suarez, David; Pantin Jackwood, Mary

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/31/2019
Publication Date: 9/12/2019
Citation: Youk, S., Lee, D., Ferreira, H.L., Afonso, C.L., Absalon, A.E., Swayne, D.E., Suarez, D.L., Pantin Jackwood, M.J. 2019. Rapid evolution of Mexican H7N3 highly pathogenic avian influenza viruses in poultry. PLoS One. 14(9):e0222457. https://doi.org/10.1371/journal.pone.0222457.
DOI: https://doi.org/10.1371/journal.pone.0222457

Interpretive Summary: Highly pathogenic avian influenza (HPAI) viruses remain a threat to poultry worldwide. Outbreaks of H7N3 HPAI have been occurring in poultry in Mexico since 2012 and vaccination has been used to control the disease. However, there is little information on the viruses causing these outbreaks. In this study, eight Mexican H7N3 HPAI viruses from 2016-2017 were isolated and fully sequenced. Phylogenetic analyses of these viruses and of previously sequenced viruses from the same lineage indicated that all eight segments of the Mexican H7N3 HPAI virus had diverged into three genetic groups by 2015. By comparing the sequences of the Mexican lineage H7N3 viruses and American ancestral wild bird AI viruses we found that the virus evolved rapidly once the virus was introduced into poultry. Continuous monitoring and molecular characterization of the H7N3 HPAI virus is important for better understanding of evolutionary dynamics and further implementing biosecurity measures including vaccination.

Technical Abstract: Outbreaks of H7N3 highly pathogenic avian influenza (HPAI) have been occurring in poultry in Mexico since 2012 and vaccination has been used to control the disease. In this study, eight Mexican H7N3 HPAI viruses from 2016-2017 were isolated and fully sequenced. No evidence of reassortment was detected with other avian influenza viruses, but phylogenetic analyses show divergence of all eight segments of the Mexican H7N3 HPAI virus from the original introduction into three genetic clusters by 2015, with 94.94 to 98.78 percent nucleotide homology of the HA genes. The HA protein of viruses from each cluster showed a different number of basic amino acids (n=5-7) in the cleavage site, and six different patterns at the predicted N-glycosylation sites. We compared the sequences of the Mexican lineage H7N3 viruses and American ancestral wild bird avian influenza (AI) viruses to characterize the virus evolutionary dynamics and found that the nucleotide substitution rates in PB2, PB1, PA, HA, NP, and NS genes greatly increased once the virus was introduced into poultry. The global nonsynonymous and synonymous ratios imply strong purifying selection driving the virus evolution. Forty-nine positively selected sites out of 171 nonsynonymous mutations were identified in the Mexican H7N3 viruses, including 7 amino acid changes observed in higher proportion in North American poultry origin AI viruses isolates than in wild bird origin viruses. Continuous monitoring and molecular characterization of the H7N3 HPAI virus is important for better understanding of evolutionary dynamics and further implementing biosecurity measures including vaccination.