Hippocrates, et al. Hippocrates on Airs, Waters and Places (Wyman & Sons, 1881).
Li, J., Lai, S., Gao, G. F. & Shi, W. The emergence, genomic diversity and global spread of SARS-CoV-2. Nature 600, 408–418 (2021).
Lee, D.-H., Bertran, K., Kwon, J.-H. & Swayne, D. E. Evolution, global spread, and pathogenicity of highly pathogenic avian influenza H5Nx clade 2.3.4.4. J. Vet. Sci. 18, 269–280 (2017).
Diseases of Poultry, 2 Volume Set, 14th Edition|Wiley. Wiley.com https://www.wiley.com/en-us/Diseases+of+Poultry%2C+2+Volume+Set%2C+14th+Edition-p-9781119371168.
Lindh, E. et al. Highly pathogenic avian influenza A(H5N1) virus infection on multiple fur farms in the South and Central Ostrobothnia regions of Finland, July 2023. Euro Surveill. Bull. Eur. Sur Mal. Transm. Eur. Commun. Dis. Bull. 28, 2300400 (2023).
Agüero, M. et al. Highly pathogenic avian influenza A(H5N1) virus infection in farmed minks, Spain, October 2022. Euro Surveill. Bull. Eur. Sur Mal. Transm. Eur. Commun. Dis. Bull. 28, 2300001 (2023).
Imai, M. et al. Experimental adaptation of an influenza H5 haemagglutinin (HA) confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Nature 486, 420–428 (2012).
Ferguson, N. M., Fraser, C., Donnelly, C. A., Ghani, A. C. & Anderson, R. M. Public health risk from the Avian H5N1 influenza epidemic. Science 304, 968–969 (2004).
Pinto, R. M. et al. BTN3A3 evasion promotes the zoonotic potential of influenza A viruses. Nature 619, 338–347 (2023).
WAHIS. World Animal Health Information Sytem. WOAH—World Organisation for Animal Health https://www.woah.org/en/home/ (2023).
Krammer, F. et al. Influenza. Nat. Rev. Dis. Primer 4, 1–21 (2018).
Huang, Z. Y. X. et al. Contrasting effects of host species and phylogenetic diversity on the occurrence of HPAI H5N1 in European wild birds. J. Anim. Ecol. 88, 1044–1053 (2019).
Lisovski, S. et al. The roles of migratory and resident birds in local avian influenza infection dynamics. J. Appl. Ecol. 55, 2963–2975 (2018).
Newman, S. H. et al. Eco-virological approach for assessing the role of wild birds in the spread of avian influenza H5N1 along the Central Asian Flyway. PLoS ONE 7, e30636 (2012).
European Food Safety Authority, European Centre for Disease Prevention and Control, European Union Reference Laboratory for Avian Influenza et al. Avian influenza overview March–April 2023. EFSA J. 21, e08039 (2023).
Fergus, R. et al. Migratory birds and avian flu. Science 312, 845–846 (2006).
cdc. Technical Report: Highly Pathogenic Avian Influenza A(H5N1) Viruses. Centers for Disease Control and Prevention https://www.cdc.gov/flu/avianflu/spotlights/2022-2023/h5n1-technical-report_june.htm (2023).
Moreno, A. et al. Asymptomatic infection with clade 2.3.4.4b highly pathogenic avian influenza A(H5N1) in carnivore pets, Italy, April 2023. Eurosurveillance 28, 2300441 (2023).
Briand, F.-X. et al. Highly pathogenic avian influenza A(H5N1) Clade 2.3.4.4b Virus in domestic cat, France, 2022. Emerg. Infect. Dis. 29, 1696–1698 (2023).
Sillman, S. J., Drozd, M., Loy, D. & Harris, S. P. Naturally occurring highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b infection in three domestic cats in North America during 2023. J. Comp. Pathol. 205, 17–23 (2023).
Domańska-Blicharz, K. et al. Outbreak of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus in cats, Poland, June to July 2023. Eurosurveillance 28, 2300366 (2023).
Songserm, T. et al. Avian influenza H5N1 in naturally infected domestic cat. Emerg. Infect. Dis. 12, 681–683 (2006).
Keawcharoen, J. et al. Avian influenza H5N1 in tigers and leopards. Emerg. Infect. Dis. 10, 2189–2191 (2004).
Lipsitch, M. et al. Viral factors in influenza pandemic risk assessment. Elife 5, e18491 (2016).
Uyeki, T. M. et al. Highly pathogenic avian influenza A(H5N1) virus infection in a dairy farm worker. N. Engl. J. Med. 390, 2028–2029 (2024).
Morin, C. W. et al. Unexplored opportunities: Use of climate- and weather-driven early warning systems to reduce the burden of infectious diseases. Curr. Environ. Health Rep. 5, 430–438 (2018).
Kjær, L. J. et al. Landscape effects and spatial patterns of avian influenza virus in Danish wild birds, 2006–2020. Transbound. Emerg. Dis. 69, 706–719 (2022).
Jung Kjær, L. et al. Using surveillance data for early warning modelling of highly pathogenic avian influenza in Europe reveals a seasonal shift in transmission, 2016–2022. Sci. Rep. 13, 15396 (2023).
Ward, M. P., Maftei, D. N., Apostu, C. L. & Suru, A. R. Association between outbreaks of highly pathogenic avian influenza subtype H5N1 and migratory waterfowl (family Anatidae) populations. Zoonoses Public Health 56, 1–9 (2009).
Belkhiria, J., Hijmans, R. J., Boyce, W., Crossley, B. M. & Martínez-López, B. Identification of high risk areas for avian influenza outbreaks in California using disease distribution models. PLoS ONE 13, e0190824 (2018).
Walsh, M. G., Amstislavski, P., Greene, A. & Haseeb, M. A. The landscape epidemiology of seasonal clustering of highly pathogenic avian influenza (H5N1) in domestic poultry in Africa, Europe and Asia. Transbound. Emerg. Dis. 64, 1465–1478 (2017).
Schreuder, J. et al. Wild bird densities and landscape variables predict spatial patterns in HPAI outbreak risk across The Netherlands. Pathog. Basel Switz. 11, 549 (2022).
Hunter, P. Europe’s worst ever bird flu outbreak. EMBO Rep. 23, e56048 (2022).
Guinat, C. et al. Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe. Virus Evol. 8, veac073 (2022).
Bergervoet, S. A., Ho, C. K. Y., Heutink, R., Bossers, A. & Beerens, N. Spread of highly pathogenic avian influenza (HPAI) H5N5 viruses in Europe in 2016–2017 appears related to the timing of reassortment events. Viruses 11, 501 (2019).
Verhagen, J. H., Fouchier, R. A. M. & Lewis, N. Highly pathogenic avian influenza viruses at the wild-domestic bird interface in Europe: Future directions for research and surveillance. Viruses 13, 212 (2021).
Chander, G., Markham, B. L. & Helder, D. L. Summary of current radiometric calibration coefficients for Landsat MSS, TM, ETM+, and EO-1 ALI sensors. Remote Sens. Environ. 113, 893–903 (2009).
Didan, K. MODIS/Terra vegetation indices 16-Day L3 global 250m SIN Grid V061. NASA EOSDIS Land Processes DAAC https://doi.org/10.5067/MODIS/MOD13Q1.061 (2021).
Aybar, C., Wu, Q., Bautista, L., Yali, R. & Barja, A. rgee: An R package for interacting with Google Earth Engine. J. Open Source Softw. 5, 2272 (2020).
Si, Y. et al. Environmental factors influencing the spread of the highly pathogenic avian influenza H5N1 virus in wild birds in Europe. Ecol. Soc. https://doi.org/10.5751/ES-03622-150326 (2010).
Ferenczi, M., Beckmann, C. & Klaassen, M. Rainfall driven and wild-bird mediated avian influenza virus outbreaks in Australian poultry. BMC Vet. Res. 17, 306 (2021).
Scolamacchia, F. et al. Different environmental gradients associated to the spatiotemporal and genetic pattern of the H5N8 highly pathogenic avian influenza outbreaks in poultry in Italy. Transbound. Emerg. Dis. 68, 152–167 (2021).
Si, Y., de Boer, W. F. & Gong, P. Different environmental drivers of highly pathogenic avian influenza H5N1 outbreaks in poultry and wild birds. PLoS ONE 8, e53362 (2013).
European Commission. Statistical Office of the European Union. EU Legislation on the 2021 Population and Housing Censuses: Explanatory Notes : 2019 Edition. (Publications Office, LU, 2019).
Fick, S. E. & Hijmans, R. J. WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).
Manaswi, N. K. Deep Learning with Applications Using Python: Chatbots and Face, Object, and Speech Recognition With TensorFlow and Keras (Apress, 2018). https://doi.org/10.1007/978-1-4842-3516-4.
Hyperparameter Tuning for Machine and Deep Learning with R: A Practical Guide. (Springer Nature, 2023). https://doi.org/10.1007/978-981-19-5170-1.
Ribeiro, M. T., Singh, S. & Guestrin, C. ‘Why Should I Trust You?’: Explaining the Predictions of Any Classifier. https://doi.org/10.48550/arXiv.1602.04938 (2016).
Lundberg, S. & Lee, S.-I. A Unified Approach to Interpreting Model Predictions. https://doi.org/10.48550/arXiv.1705.07874 (2017).
Comin, A., Stegeman, A., Marangon, S. & Klinkenberg, D. Evaluating surveillance strategies for the early detection of low pathogenicity avian influenza infections. PLoS ONE 7, e35956 (2012).
Beltrán-Alcrudo, D., Carpenter, T. E. & Cardona, C. A flock-tailored early warning system for low pathogenic avian influenza (LPAI) in commercial egg laying flocks. Prev. Vet. Med. 92, 324–332 (2009).
Guinat, C. et al. Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus H5N8 in Europe. bioRxiv https://doi.org/10.1101/2021.10.22.465255 (2021).
Śmietanka, K. et al. Highly pathogenic avian influenza H5Nx in Poland in 2020/2021: A descriptive epidemiological study of a large-scale epidemic. J. Vet. Res. 66, 1–7 (2022).
Martin, G., Becker, D. J. & Plowright, R. K. Environmental persistence of influenza H5N1 is driven by temperature and salinity: Insights from a Bayesian meta-analysis. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2018.00131 (2018).
Normile, D. Are Wild birds to blame?. Science 310, 426–428 (2005).
Trogu, T. et al. Surveillance for Avian influenza in wild birds in the Lombardy region (Italy) in the period 2022–2024. Viruses 16, 1668 (2024).
Teifke, J. P. et al. Pathology of natural infections by H5N1 highly pathogenic avian influenza virus in mute (Cygnus olor) and Whooper (Cygnus cygnus) Swans. Vet. Pathol. 44, 137–143 (2007).
Wille, M. & Barr, I. G. Resurgence of avian influenza virus. Science 376, 459–460 (2022).
European Food Safety Authority(EFSA) et al. Avian influenza overview December 2023–March 2024. EFSA J. 22, e8754 (2024).
European Food Safety Authority (EFSA) et al. Drivers for a pandemic due to avian influenza and options for One Health mitigation measures. EFSA J. 22, e8735 (2024).
Beerens, N. Genetic relationship between poultry and wild bird viruses during the highly pathogenic avian influenza H5N6 epidemic in the Netherlands, 2017–2018. Transbound. Emerg. Dis. 66, 1370–1378 (2019).
Gale, P. et al. Entry of H5N1 highly pathogenic avian influenza virus into Europe through migratory wild birds: A qualitative release assessment at the species level. J. Appl. Microbiol. 116, 1405–1417 (2014).
EFSA Panel on Animal Health and Welfare (AHAW) et al. Avian influenza. EFSA J. 15, e04991 (2017).
Globig, A. et al. Highly Pathogenic Avian Influenza H5N8 Clade 2.3.4.4b in Germany in 2016/2017. Front. Vet. Sci. https://doi.org/10.3389/fvets.2017.00240 (2018).
Mulatti, P. et al. Integration of genetic and epidemiological data to infer H5N8 HPAI virus transmission dynamics during the 2016–2017 epidemic in Italy. Sci. Rep. 8, 18037 (2018).
Klaassen, M. & Wille, M. The plight and role of wild birds in the current bird flu panzootic. Nat. Ecol. Evol. https://doi.org/10.1038/s41559-023-02182-x (2023).
Authority, E. F. S. et al. Avian influenza overview June–September 2022. EFSA J. 20, e07597 (2022).
Rijks, J. M. et al. Mass mortality caused by highly pathogenic influenza A(H5N1) virus in sandwich terns, the Netherlands, 2022. Emerg. Infect. Dis. 28, 2538–2542 (2022).
Chen, Y. & Chen, Y.-F. Global distribution patterns of highly pathogenic H5N1 avian influenza: Environmental vs. socioeconomic factors. C. R. Biol. 337, 459–465 (2014).
Peiris, J. S. M., Poon, L. L. M. & Guan, Y. Surveillance of animal influenza for pandemic preparedness. Science 335, 1173–1174 (2012).
Iglesias, I. et al. Identifying areas for infectious animal disease surveillance in the absence of population data: Highly pathogenic avian influenza in wild bird populations of Europe. Prev. Vet. Med. 96, 1–8 (2010).
Hood, G. et al. A literature review of the use of environmental sampling in the surveillance of avian influenza viruses. Transbound. Emerg. Dis. 68, 110–126 (2021).
Saavedra, I., Rabadán-González, J., Aragonés, D. & Figuerola, J. Can citizen science contribute to avian influenza surveillance?. Pathogens 12, 1183 (2023).
