Coronaviruses (CoV) infect a wide variety of hosts, causing epidemics in humans, birds, and mammals over the years. Bats (order Chiroptera) are one of the natural hosts of the Coronaviridae family. They represent 40% of the total number of mammal species in the Pantanal, a biodiversity hotspot in South America. Given the recent SARS-CoV-2 pandemic, we investigated the presence of CoV in bats captured in the Brazilian Pantanal. Oral and rectal swabs collected in 2021 from 419 bats were analyzed using Pancoronavirus-nested PCR targeting the RNA-dependent RNA-polymerase (RdRp) gene. Orthocoronavirinae was detected in 16.7% (70/419) of the bats; nine samples were sequenced, confirming that Carollia perspicillata (4), Phyllostomus hastatus (2), Desmodus rotundus (1), Molossus rufus (1), and Myotis cf. nigricans (1) collected in buildings formally used by humans were infected by Alphacoronavirus genera. This is the first description of Alphacoronavirus in bats from the Pantanal. As they are natural reservoirs of CoVs, constant monitoring of bats is important to comprehend the epidemiology of emerging viruses, especially in the Pantanal biome.

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.

Avian influenza viruses (AIVs) circulate widely among migratory birds, where frequent reassortment drives the emergence of novel genomic constellations. However, the evolutionary pathways underlying these events remain poorly understood in South America due to historically limited genomic surveillance. Here, we report the detection and evolutionary reconstruction of a low pathogenic avian influenza virus (LPAI) subtype H1N8 isolated from a White-rumped Sandpiper (Calidris fuscicollis) sampled at Lagoa do Peixe National Park (PNLP), southern Brazil, an important migratory stopover along the Atlantic Flyway. Between 2023 and 2025, 1787 samples were collected from wild birds, resulting in six AIV-positive detections during April 2024, from which one H1N8 isolate was successfully recovered and whole-genome sequenced. Genomic analyses identified a reassortant virus sharing five internal gene segments (PB2, PB1, PA, NP, and MP) with a previously described H11N2 virus detected at the same site and host species, whereas the HA, NA, and NS segments belonged to distinct South American lineages. Bayesian temporal reconstruction, discrete phylogeographic analyses, ancestral-state reconstruction, and reassortment inference consistently supported the persistence of a shared North American-derived genomic backbone followed by the acquisition of locally circulating South American gene segments. Although based on a single isolate, these findings provide an evolutionary snapshot of a reassortment event in South American migratory birds and reinforce PNLP as a key site for long-term avian influenza virus surveillance.