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

Abstract

Highly pathogenic avian influenza (HPAI) virus subtype H7N3 has been circulating in poultry in Mexico since 2012 and vaccination has been used to control the disease. In this study, eight Mexican H7N3 HPAI viruses from 2015–2017 were isolated and fully sequenced. No evidence of reassortment was detected with other avian influenza (AI) viruses, but phylogenetic analyses show divergence of all eight gene segments into three genetic clusters by 2015, with 94.94 to 98.78 percent nucleotide homology of the HA genes when compared to the index virus from 2012. 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. Comparison of the sequences of the Mexican lineage H7N3 HPAI viruses and American ancestral wild bird AI viruses to characterize the virus evolutionary dynamics showed 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 evolution of the virus. Forty-nine positively selected sites out of 171 nonsynonymous mutations were identified in the Mexican H7N3 HPAI 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 the virus evolutionary dynamics and further improving control measures including vaccination.

Characterization of commercial poultry farms in Mexico: Towards a better understanding of biosecurity practices and antibiotic usage patterns

“…The 2012 outbreak represented not only an animal health emergency but also a poultry production crisis, resulting in the death of over 22 million birds (either infected or culled), and an economic impact estimated at USD 720 million [30,33]. This H7N3 subtype has been circulating in poultry in Mexico since its first detection, causing repeated outbreaks both in commercial chickens and in backyard poultry [33][34][35][36]. Moreover, it has been suggested that Mexico could play a potential role as a hotspot for viral interchange, as it is located along various winter migration routes of wild birds [31].…”

Genetic Characterization and Pathogenesis of Avian Influenza Virus H7N3 Isolated from Spot-Billed Ducks in South Korea, Early 2019

“…The first outbreak of HPAIV caused by subtype H7N3 appeared in Pakistan in 1995 and affected 3.2 million birds, primarily breeders and boilers. Since then, it has caused outbreak in Chile (2004) [ 63 ], the Netherlands (2003) [ 64 ], British Colombia (2004) [ 65 ], and Mexico (2012) [ 66 ], causing heavy losses in the poultry industry. Although Kim et al reported the first isolations of two H7N3 strains during their 2008–2011 systemic surveillance program [ 13 ] in the Korean peninsula, detailed molecular and pathological studies from South Korea are scarce.…”

Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments

“…This sequence analysis data might support the idea that the position 105 in NP may be a determinant for host adaptation or/and increased pathogenicity. Youk et al [ 39 ] demonstrated that the Mexican H7N3 HPAI viruses, after circulating in chicken populations for several years, retained high pathogenicity to chickens but decreased fitness in mallards. Some of the changes observed in the viral genomes of Mexican H7N3 between 2012 and 2016 were associated with a point mutation at A125T in HA, NP M105V, and NP S377N [ 39 ].…”