Phylogenetic and Molecular Characterization of a Novel Reassortant High-Pathogenicity Avian Influenza A (H7N6) Virus Detected in New Zealand Poultry

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Abstract
H7 high-pathogenicity avian influenza (HPAI) virus outbreaks can cause high rates of morbidity and mortality in poultry flocks, leading to devastating impacts on poultry industries. In December 2024, an HPAI virus was detected on a poultry farm in New Zealand, being the first time a case of HPAI was reported in the country. Whole-genome sequencing, subtyping, phylogenetic, and mutation analyses were performed to characterize the virus. Results indicated a novel high-pathogenicity H7N6 avian influenza virus arose through a reassortment event between endemic low-pathogenicity H4N6 and H7 viruses, followed by two mutations at the H7 gene cleavage site. Mutation analysis suggests the novel H7N6 virus exhibits increased risk of host specificity shift, but further work is required to fully understand the functional impacts of the detected mutational events. In this instance, a timely biosecurity response was effective in eliminating the virus and preventing its transmission to secondary poultry flocks in New Zealand. However, the event underscores the critical importance of continued surveillance of commercial poultry and other potential avian carriers to facilitate early detection of low-pathogenicity avian influenza viruses, which may undergo reassortment or de novo mutation into high-pathogenicity variants.

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