Global subtype diversity, spatial distribution patterns, and phylogenetic analysis of avian influenza virus in water

Abstract

The current COVID-19 pandemic highlights the need for zoonotic infectious disease surveillance. Avian influenza virus (AIV) poses a significant threat to animal and public health due to its pandemic potential. Virus-contaminated water has been suggested as an important AIV spread mechanism among multiple species. Nevertheless, few studies have characterized the global AIV subtype diversity and distribution in environmental water. Therefore, this study aims to provide an updated descriptive and phylogenetic analysis of AIVs isolated in water samples from high risk-sites for influenza outbreaks (i.e. live bird markets, poultry farms, and wild bird habitats) on a global scale. The descriptive analysis evidenced that 21 subtypes were reported from nine countries between 2003 and 2020. Fourteen AIV subtypes were solely reported from Asian countries. Most of the viral sequences were obtained in China and Bangladesh with 47.44% and 23.93%, respectively. Likewise, the greatest global AIV subtype diversity was observed in China with 12 subtypes. Live bird markets represented the main sampling site for AIV detection in water samples (64.1%), mostly from poultry cage water. Nevertheless, the highest subtype diversity was observed in water samples from wild bird habitats, especially from the Izumi plain and the Dongting Lake located in Japan and China, respectively. Water from drinking poultry troughs evidenced the greatest subtype diversity in live bird markets; meanwhile, environmental water used by ducks had the highest number of different subtypes in poultry farms.Maximum-likelihood phylogenetic trees of hemagglutinin (HA) and neuraminidase (NA) genes showed that some sequences were closely related among different poultry/wild bird-related environments from different geographic origins. Therefore, the results suggest that even though the availability of gene sequences in public-access databases varies greatly among countries, environmental AIV surveillance represents a useful tool to elucidate potential viral diversity in wild and domestic bird populations.

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

“…Other than domestic duck species, migratory waterfowl stopover for a few days to several weeks to rest at foraging areas (wetlands and lakes) along their migratory routes ( 10 , 12 ). The AIV can spread to and from domestic duck populations due to the length of stay and wetland of both domestic and migratory duck populations, and the asymptomatic nature of infected individuals increases the likelihood that the virus will spread to other species ( 13 ). When an infected duck defecates in a specific wetland or waterbody, the AIV enters the environment and infects other ducks easily while they access the same areas.…”

Risk for waterborne transmission and environmental persistence of avian influenza virus in a wildlife/domestic interface in Mexico

“…Migratory waterfowl stopovers in proximity to backyard farms facilitate the emergence of new viral strains and enhance cross-species transmission (Müller-Theissen et al, 2022; Zhang et al, 2014). Multiple viral subtypes have been isolated from water mostly obtained in areas where farms overlap with wetlands (Das Gupta et al, 2022; Karasin et al, 2000;Mateus-Anzola et al, 2021). Therefore, household and free-range poultry on spatiotemporal coincidence with wild birds pose a high risk for in uenza outbreaks (Hassan et al, 2020).…”

Semi-Scavenging Poultry as Carriers of Avian Influenza Genes

“…As of April 2021, the records of the WHO indicated 862 human H5N1 cases from 17 different countries, including Bangladesh [7,8]. Other influenza subtypes such as H5N2, H5N3, H5N5, H5N6, H5N8, H5N9, H7N1, H7N2, H7N3, H7N7, H7N8, H7N9, and H9N2 have been isolated from different parts of the world [9,10]. It was hypothesized that the highly pathogenic H5 and H7 viruses emerged in infected chicken as a result of genetic mutations (antigenic drift or antigenic shift) in low pathogenic avian influenza (LPAI) viruses [11,12].…”