Detection of H5N1-Related PB1 Sequences in a Low Pathogenic H11N2 Virus from South American Migratory Shorebirds

Highly pathogenic avian influenza (HPAI) A(H5N1) viruses of clade 2.3.4.4b have recently spread across the Americas, prompting intensified surveillance efforts in Brazil aimed at early detection in wild birds. As part of these efforts, we identified a low pathogenic avian influenza A(H11N2) virus in a white-rumped sandpiper (Calidris fuscicollis) sampled at Lagoa do Peixe National Park (PNLP) in southern Brazil. Whole-genome sequencing revealed that seven of the eight gene segments shared high nucleotide similarity (approximately 98.8%) with viruses previously detected in shorebirds from Delaware Bay, North America. In contrast, the PB1 segment showed high nucleotide similarity (approximately 99%) to the PB1 lineage associated with clade 2.3.4.4b A(H5N1) genotype B3.2 viruses circulating in the Americas. Phylogenetic, nucleotide identity, and molecular clock analyses indicated that this lineage shares a recent common ancestor with North American LPAI viruses and was subsequently detected in distinct viral genetic backgrounds. Although no HPAI virus was identified in this study, the presence of a PB1 segment related to H5N1-associated lineages suggests that genetic components linked to these viruses were circulating among low pathogenic avian influenza viruses in South America. These findings highlight the importance of continued surveillance in migratory bird populations to improve understanding of avian influenza virus diversity and support epidemiological monitoring.