Case Report: Detection and characterization of avian influenza virus H9N2 in a broiler farm in Mozambique, 2025.

Abstract

In August 2025, Mozambique's Central Veterinary Laboratory, part of the Agricultural Research Institute, received broiler chicken carcasses for investigation after reports of elevated flock mortality. Pooled samples from the carcasses (i.e. trachea and lung) tested positive for influenza A. Subsequent subtyping ruled out hemagglutinin subtypes H5 and H7. Further analysis including tests for Newcastle disease virus, infectious bronchitis virus, infectious laryngotracheitis, and avian influenza subtype H9 confirmed the presence of H9. Whole-genome sequencing using Nanopore technology identified the virus as H9N2. Phylogenetic analysis of the hemagglutinin gene classified the virus within lineage G5.5, showing closer genetic similarity to strains circulating in the Middle East (e.g., Saudi Arabia, Jordan, and Israel) than to those in East or West Africa. This report is the first documented detection of H9N2 avian influenza in Mozambique, with significant implications for regional food security and disease management.