Epidemiology and phylodynamics of multiple clades of H5N1 circulating in domestic duck farms in different production systems in Bangladesh

Waterfowl are considered to be natural reservoirs of the avian influenza virus (AIV). However, dynamics transmission and evolutionary patterns AIV its subtypes within duck farms in Bangladesh remain poorly documented. Hence, a cross-sectional study was conducted nine districts between 2019 2021, determine prevalence H5 H9, as well identify risk factors phylodynamics H5N1 clades circulating domestic farms. The oropharyngeal cloacal swab samples were tested for Matrix gene (M-gene) followed by H5, H7, H9 using rRT-PCR. exploratory analysis performed estimate subtype different production systems, multivariable logistic regression model used that influence infection ducks. Bayesian phylogenetic generate maximum clade credibility (MCC) tree likelihood method relationships viruses isolated from detected 40% (95% CI: 33.0–48.1) highest nomadic ducks (39.8%; 95% 32.9–47.1), commercial (24.6%; 14.5–37.3) backyard (14.4%; 10.5–19.2). also (19.4%; 14.0–25.7). revealed (AOR: 2.4; 1.45–3.93), juvenile 2.2; 1.37–3.61), sick 11.59; 4.82–32.44) had higher AIV. Similarly, detection 40.8; 16.3–115.3). belong two distinct clades, 2.3.2.1a, 2.3.4.4b. 2.3.2.1a (reassorted) has been evolving silently since 2015 forming at least subgroups based on >90% posterior probability. Notably, 2.3.4.4b introduced end year 2020, which genetically similar wild birds Japan, China, Africa, indicating migration-associated an emerging panzootic clade. We recommend continuing surveillance system preventing intermingling with migratory waterfowl wetlands.