Multi-scale epidemiological dynamics of avian influenza in Bangladesh’s live poultry trading networks.

Both high and low pathogenicity avian influenza viruses (AIVs) are endemic in poultry in Bangladesh. To improve poultry health and to minimise the risk of virus spillover into humans and wild birds, we need to reduce virus prevalence and diversity. This requires an improved understanding of how different AIV lineages spread. We used a suite of molecular and virus genomic epidemiological approaches to investigate the dissemination of AIV lineages in 2021 to 2024 across various scales - nationally, between live bird markets, and within markets. Through extensive targeted sampling and sequencing, we generated over 700 new H9 and H5 AIV genomes from Bangladesh, nearly doubling the existing AIV genomic data from the country. We analysed these data using virus phylodynamic and other computational approaches. We show that high levels of virus diversity observed at markets are maintained by frequent introductions and rapid turnover of new virus lineages. At the local scale, virus movement is influenced by the structure of poultry trading networks, which vary regionally. We demonstrate differences in the national spread of duck-adapted and chicken-adapted AIVs, commensurate with differences in the production system of each species. Together, our findings highlight the potential value in improving control of virus circulation at production sites in which birds are raised, rather than focusing interventions solely at live bird markets where prevalence is typically highest. More broadly, we emphasise the value of genomic approaches in understanding how trading practices affect the diversity and spread of avian influenza and other viruses.

Carnegie, L.1, Raghwani, J.1, Mahmud, R.2, Hasan, M. 3, Dupas, M.C.4, Pinotti, F.5, Uddin, H.2, Nath, C.2, Dhar, P.K.2,6, Hasnine, I.2, Butt, S.1, Kohnle, L.7,8, Rokan, K.2, Go, Y.Y.7, Gu, G.9, Hossain, B.2, Shamim, Md.2, Das, T.2,6, Franzo, G.10, Mohsin, M.A.S.2, Judge, C.1,11, Vickers, S.1, Lewis, N.12, Mollet, B.13, Coggon, A.1,, Moores, A.13, Lewis, T.13, James, J.13 Banyard, A.C13, Brown, I.H14, Clark, B.12, Byrne, A.12,13, Galiano, M.12, Islam, A15, Sarowar, A16, Jenkins-Lynton, J.13, Conan, A.7, Pfeiffer, D.U.1,9, GCRF One Health Poultry Hub, Blake D.1, Tomley F.1, Samad MA3, Biswas, P.2, Hoque, A.H.2, Fournié, G.1,5,17, Hill SC.1. 1 Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), UK 2 Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh 3 Bangladesh Livestock Health Research Institute (BLRI), Savar, Dhaka, Bangladesh 4 Université Libre de Bruxelles (Spatial Epidemiology Lab, SpeLL), Belgium¬¬ 5 Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France 6 Charles Sturt University, Wagga Wagga, Australia 7 Centre for Applied One Health Research, City University of Hong Kong, Hong Kong SAR, China 8 European Food Safety Authority (EFSA), Parma, Italy 9 Department of Infectious Diseases and Public Health, City University of Hong Kong, Hong Kong SAR, China 10 University of Padua, Padova PD, Italy 11 London School of Hygiene & Tropical Medicine, London 12 Francis Crick Institute, London, UK 13 Animal and Plant Health Agency (APHA), Weybridge, UK 14 Pirbright Institute, Woking, Surrey UK 15 PREDICT, Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh 16 IUCN, International Union for Conservation of Nature, Bangladesh Country Office, Dhaka, Bangladesh 17 Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l’Etoile, France

Notable outbreaks, field and molecular epidemiology, and surveillance in poultry