Phylogenetic characterization
Nine IAV detected in wild dabbling ducks from the Lerma marshes were isolated in chick embryos. All eight influenza gene segments of each virus were sequenced, and the sequences were submitted into the GenBank database (Table 2).
The phylogenetic analysis of the HA gene showed three major clades. The upper clade had 3 strains (A/blue-winged_teal/EstadodeMexico/Lerma/UIFMVZ507/2017 (H5N2), A/ green-winged_teal/EstadodeMexico/Lerma/UIFMVZ80/2016 (H5N2), and A/northern_ shoveler/EstadodeMexico/Lerma/UIFMVZ613/2017 (H5N2)) related to Mexican swine and chicken sequences of H5N2 viral subtype (Figure 4). Whereas one strain (A/Mexican_duck/EstadodeMexico/Lerma/UIFMVZ377/2016 (H5N2)) was phylogenetically related to wild duck sequences of H5N1, H5N2, H5N5, and H5N9 subtypes reported in United States of America (Figure 4). The HA gene from A/blue-winged_teal/EstadodeMexico/Lerma/UIFMVZ322/2016 (H1N1) was found in a different clade, and it was strongly genetically related to U.S. and Mexican swine H1N1 viruses (Figure 4). Finally, in the lower clade were found four sequences (A/green-winged_teal/ EstadodeMexico/Lerma/UIFMVZ169/2016 (H3N2), A/green-winged_teal/EstadodeMexico/ Lerma/UIFMVZ456/2017 (H3N2), A/green-winged_teal/EstadodeMexico/Lerma/UIFMVZ 465/2017 (H3N2), and A/blue-winged_teal/EstadodeMexico/Lerma/UIFMVZ478/2017 (H3N2)) genetically similar to U.S. and Mexican swine H3N2 subtypes (Figure 4).