Background: Avian influenza viruses (genus Alphainfluenzavirus, family Orthomyxoviridae) infect avian and mammal hosts. In 2022, the high pathogenicity avian influenza virus (H5N1) spread to South America, resulting in the loss of thousands of wild birds, including endangered species, and severely impacting the global poultry industry. Objectives: We analyzed the complete genomes of influenza viruses obtained from wild birds and backyard poultry in Uruguay between February and May 2023. Methods: Twelve complete genomes were obtained in 2023 from cloacal swabs using Illumina sequencing. Genomes were phylogenetically analyzed with regional and global strains. Findings: The identified strains have multiple basic amino acids at the hemagglutinin cleavage sites, which is typical for highly pathogenic strains. The Uruguayan viruses belonged to hemagglutinin clade 2.3.4.4b of the H5N1 subtype. A reassortment in North America has resulted in some segments of South American strains being of Eurasian or North American origins. The Uruguayan viruses shared a common ancestor with South American strains from Argentina and Chile. The influenza viruses displayed a spatiotemporal divergence pattern rather than being host-specific. Main Conclusions: The arrival of the 2.3.4.4b clade in Uruguay may have been mediated by birds that acquired the virus from Argentine and Chilean waterfowl migrating in the Pacific Flyway.

The avian infectious bronchitis virus (IBV) is a highly mutable coronavirus that causes an acute and highly contagious disease responsible for economic losses to the poultry industry worldwide. Preventing and controlling bronchitis disease is difficulted by the numerous IBV circulating types with limited antigenic cross-protection that hamper the prevention and control by heterologous vaccines. The coding region of the variable spike S1 receptor-attachment domain is used to classify IBV in 7 genotypes (GI–GVII) comprising 35 viral lineages (1–35). Knowledge of the circulating IBV types causing outbreaks in a specific geographic region is beneficial to select better the appropriate vaccine(s) and contribute to disease control. In the study, 17 avian infectious bronchitis virus strains were obtained from chickens showing signs of illness in Mexico from 2007 to 2021. We detected 4 lineages within genotype I, three already known (GI-3, GI-9, GI-13) and one newly described (GI-30). In addition, we identified 2 divergent monophyletic groups that are tentatively described as lineages of new genotypes (GVIII-1 and GIX-1). Our findings revealed that Mexico's high genetic IBV diversity results from the co-circulation of divergent lineages belonging to different genotypes. Mexican IBV lineages differ significantly from Massachusetts and Connecticut vaccine strains, indicating that the currently used vaccines may need to be updated.

The avian infectious bronchitis virus (IBV) is a coronavirus that mutates frequently, leading to a contagious and acute disease that results in economic losses to the global poultry industry. Due to its genetic and serological diversity, IBV poses a challenge in preventing and controlling the pathogen. The full-length S1 sequence analysis identifies seven main genotypes (GI–GVII) comprising 35 viral lineages. In addition to the previously described lineage, a new GI lineage (GI-30) and two lineages from novel genotypes (GVIII-1 and GIX-1) have been described in Mexico. To prevent the spread of IBV outbreaks in a specific geographic location and select the suitable vaccine, it is helpful to genetically identify the circulating IBV types. Moreover, sequencing genomes can provide essential insights into virus evolution and significantly enhance our understanding of IBV variability. However, only genomes of previously described lineages (GI-1, GI-9, GI-13, and GI-17) have been reported for Mexican strains. Here, we sequenced new genomes from Mexican lineages, including the indigenous GI-30, GVIII-1, and GIX-1 lineages. Comparative genomics reveals that Mexico has relatively homogenous lineages (i.e., GI-13), some with greater variability (i.e., GI-1 and GI-9), and others extremely divergent (GI-30, GVIII-1, and GIX-1). The circulating lineages and intra-lineage variability support the unique diversity and dynamic of Mexican IBV.