Spreading of the High-Pathogenicity Avian Influenza (H5N1) Virus of Clade 2.3.4.4b into Uruguay

Abstract

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.

Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: a paradigm shift to virus transmission in South America

“…During September and early October 2023, ocular, oropharyngeal, encephalic, rectal/cloacal, and fecal swabs were obtained from pinnipeds and seabirds from different regions of the Uruguayan coastline. Samples were collected and promptly transported for molecular diagnosis (13). Clinical signs could not be determined in deceased animals.…”

“…Viral detection and HA subtyping were performed by real-time reverse transcription PCR, as previously described (13).…”

“…Amplicons were pooled and purified using AMPure XP (Beckman Coulter, Indianapolis, IN, USA), and 100 ng were subjected to the Nextera™ DNA Flex Library Preparation kit (Illumina, San Diego, CA, USA) employing a unique dual indexing (XT-Index Kit V2-Set A). Libraries quantification and sequencing were performed as previously reported (13).…”

“…There is no evidence of reassortment events in the dataset, supporting the fact that all South American strains (n=162) were derived from strains with a single segment composition that successfully spread in South America. The 4:4 reassortant viruses, with segments derived from both North American (PB2, PB1, NP, and NS) and Eurasian (PA, HA, N, A, and M) lineages (12,13,20) The South American dataset showed low sequence variability, with fewer informative phylogenetic sites per segment. We concatenated all coding sequences (CDS) for the genomes to augment the phylogenetic signal.…”

“…In October 2022, it emerged in Latin America, with severe outbreaks identified in Chile, Colombia, Ecuador, Mexico, Peru, and Venezuela (10)(11)(12). In Uruguay, HPAIV H5N1 was detected in wild birds and backyard poultry from February to May 2023 (13).…”