Outbreak of H9N2 avian influenza viruses in lesser rhea in Peru, June-July 2025

Abstract

Avian influenza viruses (AIVs) are endemic in the Americas and responsible for outbreaks in both domestic and wild birds that occasionally spill over into humans. We report the first known outbreak of AIV H9N2 in lesser rhea (Rhea pennata), also known as Darwins rhea, in the region of Puno-Peru. The animals in this study lived in an isolated conservation center located in remote highlands above 4,000 m.a.s.l. Between June and July 2025, a total of 46/92 animals were recorded sick, with symptoms including greenish diarrhea (100%), hyporexia (24%), dyspnea (76%), nasal discharge (42%), drowsiness (18%) and isolation from the flock (73%), and 94% later died. Gross pathology exams revealed septicemia characterized by severe hepatitis, pneumonia, tracheitis, enteritis, and encephalitis. Swab and necropsy samples tested positive for Influenza A by PCR and were later identified as H9N2 through whole genome sequencing. We generated complete H9N2 genomes for two individuals. No additional pathogens were found. Phylogenetic analysis across all eight segments revealed that the viruses were low pathogenicity H9N2 AIV strains of North American origin, which indicated this outbreak was a new introduction of the virus into South America. We also performed a comparative mutational analysis and identified multiple mutations previously associated with mammalian host adaptation, increased virulence, increased pathogenicity, and increased virus binding to 2-6 receptors, which may explain the high mortality rates observed despite the supposedly low pathogenicity of the strain. We also identified novel mutations specific to rhea viruses that will need to be experimentally validated. This is the first report of a natural H9N2 systemic infection in an avian host, highlighting a need for increased surveillance efforts for zoonotic influenza viruses with pandemic potential. Author SummaryAvian influenza viruses (AIVs) are endemic in the Americas and cause more than 7,600 infections annually in domestic and wild birds worldwide each year. We report detection of AIV H9N2 in lesser rhea during an outbreak that occurred in June-July 2025 in the Andean highlands of Puno in Peru. Multiple sick animals were reported with symptoms of respiratory and gastrointestinal disease and 94% of them later died. Samples collected tested positive for Influenza A and they were subtyped as H9N2 of low pathogenic origin from North America. This is the third time H9N2 enters South America from North America, presumably through wild birds, some of which migrate along the Pacific Flyway. Comparison with other H9N2 sequences revealed a total of 44 mutations of interest that may explain the elevated death rates observed. Surveillance in wild birds remains patchy at best and needs to be strengthened in order to prevent spillover events into other animals, including humans.