Phylogenetic analysis, molecular changes, and adaptation to chickens of Mexican lineage H5N2 low-pathogenic avian influenza viruses from 1994 to 2019

Authors: YOUK, SUNGSU - Orise Fellow; LEYSON, CHRISTINA - Orise Fellow; PARRIS, DARREN - Orise Fellow; KARIITHI, HENRY - Orise Fellow; Suarez, David; Pantin Jackwood, Mary

Submitted to: Transboundary and Emerging Diseases
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/8/2022
Publication Date: 3/4/2022
Citation: Youk, S., Leyson, C., Parris, D., Kariithi, H., Suarez, D.L., Pantin Jackwood, M.J. 2022. Phylogenetic analysis, molecular changes, and adaptation to chickens of Mexican lineage H5N2 low-pathogenic avian influenza viruses from 1994 to 2019. Transboundary and Emerging Diseases. https://doi.org/10.1111/tbed.14476.
DOI: https://doi.org/10.1111/tbed.14476

Interpretive Summary: Avian influenza (AI) are a threat to poultry worldwide. The Mexican lineage H5N2 low pathogenic avian influenza viruses (LPAIV) continue to cause losses in poultry in Mexico and other countries. In this study we sequenced the full genome of forty-nine H5N2 LPAIVs isolated from 1994 to 2019. Analyses of these sequences showed genetic reassortment between two separate groups of H5N2 viruses. Furthermore, the recent H5N2 viruses reassorted with previously unidentified avian influenza viruses. We also examined the pathogenicity of two H5N2 LPAIV in birds and found that the more recent virus was more infectious and transmitted better in chickens. The genetic changes that occur as this lineage of H5N2 LPAIVs continues circulating in poultry is concerning not only because of the effect of these changes on vaccination efficacy, but also because of the potential of the viruses to mutate to the highly pathogenic form. Continued vigilance and surveillance efforts and the pathogenic and genetic characterization of circulating viruses are required for the effective control of this virus.

Technical Abstract: The Mexican lineage H5N2 low pathogenic avian influenza viruses (LPAIVs) were first detected in 1994 and mutated to highly pathogenic avian influenza viruses (HPAIVs) in 1994-1995 causing widespread outbreaks in poultry. By using vaccination and other control measures, the HPAIVs were eradicated but the LPAIVs continued circulating in Mexico and spread to several other countries. To get better resolution of the phylogenetics of this virus, the full genome sequences of 44 H5N2 LPAIVs isolated from 1994 to 2011, and 6 detected in 2017 and 2019, were analysed. Phylogenetic incongruence demonstrated genetic reassortment between two separate groups of the Mexican lineage H5N2 viruses between 2005 and 2010. Moreover, the recent H5N2 viruses reassorted with previously unidentified avian influenza viruses. Bayesian phylogeographic results suggested that mechanical transmission involving human activity is the most probable cause of the virus spillover to Central American, Caribbean, and East Asian countries. Increased infectivity and transmission of a 2011 H5N2 LPAIV in chickens compared to a 1994 virus demonstrates improved adaptation to chickens, while low virus shedding, and limited contact transmission was observed in mallards with the same 2011 virus. The sporadic increase in basic amino acids in the HA cleavage site, changes in potential N-glycosylation sites in the HA, and truncations of PB1-F2 should be further examined in relation to the increased infectivity and transmission in poultry. The genetic changes that occur as this lineage of H5N2 LPAIVs continues circulating in poultry is concerning not only because of the effect of these changes on vaccination efficacy, but also because of the potential of the viruses to mutate to the highly pathogenic form. Continued vigilance and surveillance efforts, and the pathogenic and genetic characterization of circulating viruses, are required for the effective control of this virus.