Genetic reassortment and diversification of host specificity have driven evolutionary trajectories of lineages of panzootic H5N1 influenza

Harvey, W. T.; Pinto, R. M.; Brown, M. D.; Lu, L.; Quantrill, J. L.; Yang, J.; Pankaew, N.; Nel, M.; Baxter, J.; Byrne, A. M. P.; Kapczynski, D. R.; Iqbal, M.; James, J.; Banyard, A. C.; Brown, I.; Barclay, W.; Peacock, T. P.; Digard, P.; Lycett, S. J.

doi:10.1101/2025.08.20.670882

bioRxiv · 10.1101/2025.08.20.670882

Genetic reassortment and diversification of host specificity have driven evolutionary trajectories of lineages of panzootic H5N1 influenza

Harvey, W. T.·Pinto, R. M.·Brown, M. D.·Lu, L.·Quantrill, J. L.·Yang, J.·Pankaew, N.·Nel, M.·Baxter, J.·Byrne, A. M. P.·Kapczynski, D. R.·Iqbal, M.·James, J.·Banyard, A. C.·Brown, I.·Barclay, W.·Peacock, T. P.·Digard, P.·Lycett, S. J.

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Abstract

Since 2021, subclade 2.3.4.4b A(H5N1) high pathogenicity avian influenza (HPAI) viruses have undergone changes in ecology and epidemiology, causing a panzootic of unprecedented scale in wild and domestic birds with spill-over infections and perceptible transmission in a range of mammalian species, raising concern over zoonotic potential. HPAI viruses readily exchange gene segments with low pathogenicity avian influenza viruses via reassortment, a mechanism that facilitates pronounced phenotypic change. Observations suggest changes in the seasonality and host range of panzootic viruses, however, data on the role of reassortment in determining such features are limited. Using phylodynamic approaches, we describe the emergence of the panzootic lineage and using a novel global genotype classification system we describe the subsequent emergence and global structuring of genotypes generated by reassortment. Focusing on evolutionary dynamics in Europe, we show reassortment has produced high fitness genotypes with enhanced capacity for transmission and further we show such advantages can be host-dependent, contrasting successful generalist genotypes with a specialist lineage (EA-2022-BB) adapted to birds of the order Charadriiformes. Experimental investigation of NS1-mediated shutoff indicates this Charadriiformes-specialist does not inhibit host cellular gene expression and hamper the defences of more typical hosts such as water- and land-fowl. We attribute this primarily to variation at position 127 of the NS1 protein. Our results emphasise that reassortment has driven phenotypic change, affected viral fitness, and caused diversification of host specificity and seasonality. Such factors should be considered in studies that seek to identify drivers of HPAI spread and map spillover risk. Additionally, relaxation of host specialisation, ecological diversification, and potential endemicity in atypical host populations present new reassortment opportunities that could result in further novel phenotypes.

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Harvey, W. T., Pinto, R. M., Brown, M. D., Lu, L., Quantrill, J. L., Yang, J., Pankaew, N., Nel, M., Baxter, J., Byrne, A. M. P., Kapczynski, D. R., Iqbal, M., James, J., Banyard, A. C., Brown, I., Barclay, W., Peacock, T. P., Digard, P., Lycett, S. J.. 2025-08-20. Genetic reassortment and diversification of host specificity have driven evolutionary trajectories of lineages of panzootic H5N1 influenza. https://doi.org/10.1101/2025.08.20.670882

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