#19,159
Although we spend a good deal of time looking at the Asian-lineage of LPAI H9N2, which has become particularly well adapted to poultry and which continues to spill over into humans (particularly in China), we rarely hear about it in North or South America.
In 2019's A Global Perspective on H9N2 Avian Influenza Virus, the authors summed up its impact on the Western Hemisphere:
As we've discussed often (see Cell: Early-warning Signals and the Role of H9N2 in the Spillover of Avian Influenza Viruses) LPAI H9N2 is famous for its ability to reassort with other influenza subtypes, often enhancing HPAI viruses with improved transmissibility or replication in mammals.2.1.6. The Americas
H9N2 viruses have been isolated from poultry in the USA periodically throughout the second half of the twentieth Century, in fact the prototypic H9N2 isolate (A/turkey/Wisconsin/1/1966) was isolated in this period. All isolated viruses have been of the American lineage and appear to be spillover events from wild birds, possibly sea birds which carry genetically closely related viruses in this region. Since 2001, there has been no evidence of the virus in poultry in North America, despite routine surveillance and extensive evidence of other non-H9N2 viruses in poultry [64,65,66,67,68].
In South America, there is serological evidence from 2005 of H9N2 infections in Colombia, however, no virus was isolated and no further evidence has been reporter since [66].
And, in addition to birds, LPAI H9N2 has a track record of infecting humans, pigs, and even bats (see Preprint: The Bat-borne Influenza A Virus H9N2 Exhibits a Set of Unexpected Pre-pandemic Features).
All of which makes the following preprint - about a particularly virulent strain of (still LPAI) H9N2 spreading through a remote Rhea Conservation Center in Southern Peru - more than a little interesting.
Outbreak of H9N2 avian influenza viruses in lesser rhea in Peru, June-July 2025
Alejandra Garcia-Glaessner, Alvin Crespo-Bellido, Breno Muñoz-Saavedra, Diana Juarez, Patricia Barrera, Gabriela Salmon-Mulanovich, Shadam E. Checahuari-Jarata, Dany Cruz, Dennis X. Huisa-Balcon, Grover Idme, Martha L. Nelson, Jesus Lescano, Mariana Leguia
doi: https://doi.org/10.64898/2026.05.08.723762This article is a preprint and has not been certified by peer review
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 Darwin’s 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 α2-6 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.
(SNIP)A larger concern is the potential for H9N2 AIVs to create reassortants with locally circulating strains that could make them especially well adapted to mammals [76]. H9N2 has been reported in bats during routine surveillance efforts in Egypt and South Africa [77,78], further highlighting the host range of this subtype.
The introduction of a new strain of H9N2 is therefore of particular concern, as it is a well-recognized donor of internal gene segments that have contributed to the emergence of other influenza strains through reassortment [79].
The limited availability of H9N2 sequences from South America remains a significant challenge for interpreting regional viral evolution. This is the first reported outbreak of LPAI H9N2 in lesser rheas and provides genomic evidence of a distinct introduction of this subtype of AIV into South America.
Our findings expand our current knowledge of H9N2 host range in a high altitude environment and provide evidence that low pathogenicity strains can result in high mortality rates, perhaps linked to specific viral mutations.
Surveillance programs need to be strengthened to incorporate broad monitoring for circulating AIVs in both poultry and wild birds to enable early detection and close monitoring of regional virus circulation, cross-species transmission, viral evolution, genetic adaptation and future risk assessment.
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| Range Of Endemic H9N2 Viruses |
Although some attempts have been made at controlling the H9N2 virus (including using largely ineffective vaccines) - since it produces relatively mild illness in poultry - it is often tolerated or ignored.
While H9N2 remains far from our biggest pandemic concern, the CDC has designated 2 different lineages (A(H9N2) G1 and A(H9N2) Y280) as having at least some pandemic potential (see CDC IRAT SCORE), and several candidate vaccines have been developed.
And many will be surprised to see that, in terms of risk of emergence, the H9N2 Y280 lineage is ranked higher than H5N1, while the G1 lineage is ranked only slightly lower.
