First detection of an H5N2 subtype of Influenza A virus detected in Charadrius collaris from the Brazilian Pantanal

The migratory bird orders Anseriformes and Charadriiformes are natural reservoirs of avian influenza virus (AIV) and key contributors to its global dissemination. Stopover and wintering areas used by these species are critical hotspots for virus transmission, underscoring the need for routine surveillance. The Pantanal biome in central South America-an extensive floodplain crossed by two major intercontinental migratory routes-hosts numerous species of migratory birds. Given the ecological relevance of this biome and the health risks associated with AIV, this study aimed to investigate AIV circulation in the region. A total of 1,108 orotracheal and cloacal swab samples from 157 bird species were analyzed using RT-qPCR targeting the matrix gene of AIV. Influenza A virus RNA was detected in Charadrius collaris. Subsequent sequencing of the HA and NA genes revealed 94% similarity with H5N2 strains previously identified in Colombian Anatidae in 2011. Additional gene segments (NP;NS;PA;M;PB1;PB2) showed similarity to strains from America and Asia continents. This is the first report of an AIV-infected bird in the Brazilian Pantanal and confirms the presence of a low-pathogenic H5N2 subtype. The findings highlight the role of migratory birds in viral dissemination inland and the potential role of resident species as local reservoirs.