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

Characterization of the avian influenza viruses distribution in the environment of live poultry market in China, 2019-2023

BACKGROUND

The prevalence and transmission of avian influenza viruses (AIVs) in the live poultry market (LPM) is a serious public health concern. This study was to investigate the prevalence of different subtypes of avian influenza viruses in environment of LPM, and to analyze the differences and seasonality of the nucleic acid positive rate (NAPR) of A type, H5, H7, and H9 subtypes in feces, sewage, drinking water, breeding cages, and chopping boards.

METHODS

Feces, breeding cages swabs, drinking water, sewage and chopping boards swabs were collected from live poultry market during 2019-2023 from southern and northern China. Real-time PCR was used to screen for virus subtypes. Viruses were isolated, and deep sequencing was performed to obtain whole-genome sequences. Chi-square test was used for statistical analysis of categorical variable, GraphPad Prism software were used to construct graphs.

RESULTS

A total of 64,599 environmental samples were collected from live poultry markets in the southern China and northern China between 2019 and 2023. The average NAPR of the A type was significantly higher in the samples collected from the southern China than in those collected from the northern China (P < 0.05). The NAPR of H5, H7, and H9 subtypes carried by the five types of environmental samples in the southern China were significantly different (P < 0.05), and a higher NAPR was detected in chopping boards (10.84%), breeding cages (0.28%), and drinking water (40.97%) respectively. The average NAPR of the H9 and H5 subtypes displayed seasonality, reaching a peak in January and February in the southern China, while the peak of the H9 subtype was from October to February in the northern China. A total of 19 subtypes were identified. The H5 subtype significantly decreased, the H7 subtype was almost undetectable, and other subtypes, such as the H3 subtype, increased.

CONCLUSIONS

The highly pathogenic H5 subtype has significantly decreased in the live poultry market in China since 2022. However, the proportion of some subtypes, such as the H3 subtype, with low pathogenicity to poultry, has increased, while the H9 subtype remains at a high level. It must be noted that these low pathogenic avian influenza viruses often have no obvious symptoms, can circulate asymptomatically in infected poultry, and are highly pathogenic to humans. Our findings provide insights into the control and prevention of avian influenza viruses and the risk of pandemics associated with avian influenza viruses in the live poultry market.

Risk for Waterborne Transmission and Environmental Persistence of Avian Influenza Virus in a Wildlife/Domestic Interface in Mexico

Aquatic habitats provide a bridge for influenza transmission among wild and domestic species. However, water sources pose highly variable physicochemical and ecological characteristics that affect avian influenza virus (AIV) stability. Therefore, the risk of survival or transmissibility of AIV in the environment is quite variable and has been understudied. In this study, we determine the risk of waterborne transmission and environmental persistence of AIV in a wild/domestic bird interface in the Central Mexico plateau (North America) during the winter season using a multi-criteria decision analysis (MCDA). A total of 13 eco-epidemiological factors were selected from public-access databases to develop the risk assessment. The MCDA showed that the Atarasquillo wetland presents a higher persistence risk in January. Likewise, most of the backyard poultry farms at this wild-domestic interface present a high persistence risk (50%). Our results suggest that drinking water may represent a more enabling environment for AIV persistence in contrast with wastewater. Moreover, almost all backyard poultry farms evidence a moderate or high risk of waterborne transmission especially farms close to water bodies. The wildlife/domestic bird interface on the Atarasquillo wetland holds eco-epidemiological factors such as the presence of farms in flood-prone areas, the poultry access to outdoor water, and the use of drinking-water troughs among multiple animal species that may enhance waterborne transmission of AIV. These findings highlight the relevance of understanding the influence of multiple factors on AIV ecology for early intervention and long-term control strategies.

Geospatial and Temporal Analysis of Avian Influenza Risk in Thailand: A GIS-Based Multi-Criteria Decision Analysis Approach for Enhanced Surveillance and Control

Avian influenza (AI) is a viral infection that profoundly affects global poultry production. This study aimed to identify the spatial and temporal factors associated with AI in Thailand, using a geographic information system (GIS)-based multi-criteria decision analysis (MCDA) approach. We discovered that high-risk areas for AI were primarily concentrated in the central and lower northern regions of the country, with fewer occurrences in the northeastern and southern regions. Model validation using historical outbreak data showed moderate agreement (AUC = 0.60, 95% CI = 0.58-0.61). This study provides valuable insights for planning national AI surveillance programs and aiding in disease prevention and control efforts. The efficiency and effectiveness of disease surveillance at the national level can be improved using this GIS-based MCDA, in conjunction with temporal risk factor analysis.

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

Semi-Scavenging Poultry as Carriers of Avian Influenza Genes

Ducks are the natural reservoir of influenza A virus and the central host for the avian influenza virus (AIV) subtype H5N1, which is highly pathogenic. Semi-scavenging domestic ducks allow for the reemergence of new influenza subtypes which could be transmitted to humans. We collected 844 cloacal swabs from semi-scavenging ducks inhabiting seven migratory bird sanctuaries of Bangladesh for the molecular detection of avian influenza genes. We detected the matrix gene (M gene) using real-time RT-PCR (RT-qPCR). Subtyping of the AIV-positive samples was performed by RT-qPCR specific for H5, H7, and H9 genes. Out of 844 samples, 21 (2.488%) were positive for AIV. Subtyping of AIV positive samples (n = 21) revealed that nine samples (42.85%) were positive for the H9 subtype, five (23.80%) were positive for H5, and seven (33.33%) were negative for the three genes (H5, H7, and H9). We detected the same genes after propagating the virus in embryonated chicken eggs from positive samples. Semi-scavenging ducks could act as carriers of pathogenic AIV, including the less pathogenic H9 subtype. This can enhance the pathogenicity of the virus in ducks by reassortment. The large dataset presented in our study from seven areas should trigger further studies on AIV prevalence and ecology.