A literature review of the use of environmental sampling in the surveillance of avian influenza viruses

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.

Evolution and biological characteristics of H11 avian influenza viruses isolated from migratory birds and pigeons

The emergence of novel avian influenza reassortants in wild birds in recent years is a public health concern. However, the viruses that circulate in migratory birds are not fully understood. In this study, we summarized and categorized global H11 avian influenza viruses and reported that waterfowl and shorebirds are the major reservoirs of the identified H11 viruses. The surveillance data of the 35,749 faecal samples collected from wild bird habitats in eastern China over the past seven years revealed a low prevalence of H11 viruses in birds, with a positive rate of 0.067% (24 isolates). The phylogenetic analysis of the twenty viruses indicated that H11 viruses have undergone complex reassortment with viruses circulating in waterfowl and shorebirds. These tested viruses do not acquire mammalian adaptive mutations in their genomes and preferentially bind to avian-type receptors. Experimental infection studies demonstrated that the two tested H11N9 viruses of wild bird origin replicated and transmitted more efficiently in ducks than in chickens, whereas the pigeon H11N2 virus isolated from a live poultry market was more adapted to replicate in chickens than in ducks. In addition, some H11 isolates replicated efficiently in mice and caused body weight loss but were not lethal. Our study revealed the role of waterfowl and shorebirds in the ecology and evolution of H11 viruses and the potential risk of introducing circulating H11 viruses into ducks or chickens, further emphasizing the importance of avian influenza surveillance at the interface of migratory birds and poultry.

Wastewater monitoring of human and avian influenza A viruses in Northern Ireland: a genomic surveillance study

BACKGROUND

Influenza A viruses (IAVs) are significant pathogens of humans and other animals. Although endemic in humans and birds, novel IAV strains can emerge, jump species, and cause epidemics, like the latest variant of H5N1. Wastewater-based epidemiology (WBE) has been shown capable of detecting human IAVs. We aimed to assess whether whole-genome sequencing (WGS) of IAVs from wastewater is possible and can be used to discriminate between circulating strains of human and any non-human IAVs, such as those of avian origin.

METHODS

Using a pan-IAV RT-quantitative PCR assay, six wastewater treatment works (WWTWs) across Northern Ireland were screened from Aug 1 to Dec 5, 2022. A nanopore WGS approach was used to sequence RT-qPCR-positive samples. Phylogenetic analysis of sequences relative to currently circulating human and non-human IAVs was performed. For comparative purposes, clinical data (PCR test results) were supplied by The Regional Virus Laboratory, Belfast Health and Social Care Trust (Belfast, Northern Ireland, UK).

FINDINGS

We detected a dynamic IAV signal in wastewater from Sept 5, 2022, onwards across Northern Ireland, which did not show a clear positive relationship with the clinical data obtained for the region. Meta (mixed strain) whole-genome sequences were generated from wastewater samples displaying homology to only human and avian IAV strains. The relative proportion of IAV reads of human versus avian origin differed across time and sample site. A diversity in subtypes and lineages was detected (eg, H1N1, H3N2, and several avian). Avian segment 8 related to those found in recent H5N1 clade 2.3.4.4b was identified.

INTERPRETATION

WBE affords a means to monitor circulating human and avian IAV strains and provide crucial genetic information. As such, WBE can provide rapid, cost-effective, year-round One Health surveillance to help control IAV epidemic and pandemic-related threats. However, optimisation of WBE protocols are necessary to ensure observed wastewater signals not only correlate with clinical case data, but yield information on the wider environmental pan-influenz-ome.

FUNDING

Department of Health for Northern Ireland.

Effect of stabilizers on the detection of swine influenza A virus (swIAV) in spiked oral fluids over time

BACKGROUND

Aggregated samples such as oral fluids (OFs) display an animal friendly and time and cost-efficient sample type for swine Influenza A virus (swIAV) monitoring. However, further molecular and biological characterization of swIAV is of particular significance. The reportedly inferior suitability of aggregated samples for subtyping of swIAV presents a major drawback compared to nasal swabs, still considered the most appropriate sample type for this purpose (Garrido-Mantilla et al. BMC Vet Res 15(1):61, 2019). In addition, the viral load in the original sample, storage conditions and characteristics of different swIAV strains might further compromise the eligibility of aggregated samples for molecular detection and subtyping. Therefore, the present study aimed to evaluate the suitability of stabilizing media to minimize the degradation of viral RNA and thus increase the detection and subtyping rate of swIAV by RT-qPCR in spiked OFs under different conditions (virus strain, storage temperature and viral load in the original sample) over a time span of 14 days.

RESULTS

The use of stabilizing media in spiked OFs resulted in a significant higher probability to detect swIAV RNA compared to OFs without stabilizers (OR = 46.1, p < 0.001). In addition, swIAV degradation over time was significantly reduced in samples suspended with stabilizer (OR = 5.80, p < 0.001), in samples stored at 4 °C (OR = 2.53, p < 0.001) and in samples spiked with the avian derived H1N2 subtype (OR = 2.26, p < 0.01). No significant differences in swIAV RNA detection and degradation of swIAV RNA in spiked OFs over time were observed between the three different stabilizing media.

CONCLUSION

Addition of stabilizers and storage of samples under cooled conditions significantly improved detection and subtyping of swIAV in spiked OFs.

Avian Influenza: Lessons from Past Outbreaks and an Inventory of Data Sources, Mathematical and AI Models, and Early Warning Systems for Forecasting and Hotspot Detection to Tackle Ongoing Outbreaks

BACKGROUND/OBJECTIVES

The ongoing avian influenza (H5N1) outbreak, one of the most widespread and persistent in recent history, has significantly impacted public health and the poultry and dairy cattle industries. This review covers lessons from past outbreaks, risk factors for transmission, molecular epidemiology, clinical features, surveillance strategies, and socioeconomic impacts. Since 1997, H5N1 has infected over 900 individuals globally, with a fatality rate exceeding 50%. Key factors influencing infection rates include demographic, socioeconomic, environmental, and ecological variables. The virus's potential for sustained human-to-human transmission remains a concern. The current outbreak, marked by new viral clades, has complicated containment efforts.

METHODS

This review discusses how to integrate technological advances, such as mathematical modeling and artificial intelligence (AI), to improve forecasting, hotspot detection, and early warning systems.

RESULTS

We provide inventories of data sources, covering both conventional and unconventional data streams, as well as those of mathematical and AI models, which can be vital for comprehensive surveillance and outbreak responses.

CONCLUSION

In conclusion, integrating AI, mathematical models, and technological innovations into a One-Health approach is essential for improving surveillance, forecasting, and response strategies to mitigate the impacts of the ongoing avian influenza outbreak. Strengthening international collaboration and biosecurity measures will be pivotal in controlling future outbreaks and protecting both human and animal populations from this evolving global threat.

Avian Influenza outbreaks: Human infection risks for beach users - One health concern and environmental surveillance implications

Despite its popularity for water activities, such as swimming, surfing, fishing, and rafting, inland and coastal bathing areas occasionally experience outbreaks of highly pathogenic avian influenza virus (HPAI), including A(H5N1) clade 2.3.4.4b. Asymptomatic infections and symptomatic outbreaks often impact many aquatic birds, which increase chances of spill-over events to mammals and pose concerns for public health. This review examined the existing literature to assess avian influenza virus (AIV) transmission risks to beachgoers and the general population. A comprehensive understanding of factors governing such crossing of the AIV host range is currently lacking. There is limited knowledge on key factors affecting risk, such as species-specific interactions with host cells (including binding, entry, and replication via viral proteins hemagglutinin, neuraminidase, nucleoprotein, and polymerase basic protein 2), overcoming host restrictions, and innate immune response. AIV efficiently transmits between birds and to some extent between marine scavenger mammals in aquatic environments via consumption of infected birds. However, the current literature lacks evidence of zoonotic AIV transmission via contact with the aquatic environment or consumption of contaminated water. The zoonotic transmission risk of the circulating A(H5N1) clade 2.3.4.4b virus to the general population and beachgoers is currently low. Nevertheless, it is recommended to avoid direct contact with sick or dead birds and to refrain from bathing in locations where mass bird mortalities are reported. Increasing reports of AIVs spilling over to non-human mammals have raised valid concerns about possible virus mutations that lead to crossing the species barrier and subsequent risk of human infections and outbreaks.

Pathogen Surveillance in Swallows (family Hirundinidae): Investigation into Role as Avian Influenza Vector in Eastern Canada Agricultural Landscapes

First detected in Atlantic Canada in December 2021, highly pathogenic avian influenza virus (HPAIV) subtype H5N1 clade 2.3.4.4b, A/Goose/Guangdong/1/96 lineage, has caused massive mortality in wild birds and domestic poultry in North America. Swallows (Hirundinidae), abundant in North American agricultural ecosystems, have been proposed as possible (bridge) species for HPAIV transmission between wild and domestic birds. We aimed to seek evidence of the potential role of swallows in bridging AIV infection between wild bird reservoirs and poultry flocks in eastern Canada. During a wide-scale outbreak of HPAIV in wild birds and poultry farms across eastern Canada, 200 samples were collected from swallow breeding sites in the Canadian provinces of New Brunswick, Nova Scotia, Ontario, and Quebec, June-August 2022. Samples came from Barn Swallow (Hirundo rustica; n=142), Tree Swallow (Tachycineta bicolor; n=56), and Cliff Swallow (Petrochelidon pyrrhonota; n=2) nests. All samples tested negative for AIV, suggesting that HPAIV and low pathogenic AIV (LPAIV) strains were probably not circulating widely in swallows during the 2022 breeding season in eastern Canada; thus swallows may present a low risk of transmitting AIV. Within a management context, these findings suggest that removing nests of Barn Swallows, a species at risk in Canada, from the exterior of biosecure domestic poultry facilities may not significantly reduce risks of HPAI transmission to poultry.

Isolation and genetic characteristics of Novel H4N1 Avian Influenza viruses in ChongQing, China

BACKGROUND

Avian influenza viruses (AIVs) constitute significant zoonotic pathogens encompassing a broad spectrum of subtypes. Notably, the H4 subtype of AIVs has a pronounced ability to shift hosts. The escalating prevalence of the H4 subtype heightens the concern for its zoonotic potential, signaling an urgent need for vigilance.

METHODS

During the period from December 2021 to November 2023, we collected AIV-related environmental samples and assessed them using a comprehensive protocol that included nucleic acid testing, gene sequencing, isolation culture, and resequencing.

RESULTS

In this study, a total of 934 environmental samples were assessed, revealing a remarkably high detection rate (43.66%, 289/662) of AIV in the live poultry market. Notably, the H4N1 subtype AIV (cs2301) was isolated from the live poultry market and its complete genome sequence was successfully determined. Subsequent analysis revealed that cs2301, resulting from a reassortment event between wild and domesticated waterfowl, exhibits multiple mutations and demonstrates potential for host transfer.

CONCLUSIONS

Our research once again demonstrates the significant role of wild and domesticated waterfowl in the reassortment process of avian influenza virus, enriching the research on the H4 subtype of AIV, and emphasizing the importance of proactive monitoring the environment related to avian influenza virus.

Genetic Diversity of Avian Influenza Viruses Detected in Waterbirds in Northeast Italy Using Two Different Sampling Strategies

Avian influenza viruses (AIVs), which circulate endemically in wild aquatic birds, pose a significant threat to poultry and raise concerns for their zoonotic potential. From August 2021 to April 2022, a multi-site cross-sectional study involving active AIV epidemiological monitoring was conducted in wetlands of the Emilia-Romagna region, northern Italy, adjacent to densely populated poultry areas. A total of 129 cloacal swab samples (CSs) and 407 avian faecal droppings samples (FDs) were collected, with 7 CSs (5.4%) and 4 FDs (1%) testing positive for the AIV matrix gene through rRT-PCR. A COI-barcoding protocol was applied to recognize the species of origin of AIV-positive FDs. Multiple low-pathogenic AIV subtypes were identified, and five of these were isolated, including an H5N3, an H1N1, and three H9N2 in wild ducks. Following whole-genome sequencing, phylogenetic analyses of the hereby obtained strains showed close genetic relationships with AIVs detected in countries along the Black Sea/Mediterranean migratory flyway. Notably, none of the analyzed gene segments were genetically related to HPAI H5N1 viruses of clade 2.3.4.4b isolated from Italian poultry during the concurrent 2021-2022 epidemic. Overall, the detected AIV genetic diversity emphasizes the necessity for ongoing monitoring in wild hosts using diverse sampling strategies and whole-genome sequencing.

Targeted genomic sequencing of avian influenza viruses in wetland sediment from wild bird habitats

Diverse influenza A viruses (IAVs) circulate in wild birds, including highly pathogenic strains that infect poultry and humans. Consequently, surveillance of IAVs in wild birds is a cornerstone of agricultural biosecurity and pandemic preparedness. Surveillance is traditionally done by testing wild birds directly, but obtaining these specimens is labor intensive, detection rates can be low, and sampling is often biased toward certain avian species. As a result, local incursions of dangerous IAVs are rarely detected before outbreaks begin. Testing environmental specimens from wild bird habitats has been proposed as an alternative surveillance strategy. These specimens are thought to contain diverse IAVs deposited by a broad range of avian hosts, including species that are not typically sampled by surveillance programs. To enable this surveillance strategy, we developed a targeted genomic sequencing method for characterizing IAVs in these challenging environmental specimens. It combines custom hybridization probes, unique molecular index-based library construction, and purpose-built bioinformatic tools, allowing IAV genomic material to be enriched and analyzed with single-fragment resolution. We demonstrated our method on 90 sediment specimens from wetlands around Vancouver, Canada. We recovered 2,312 IAV genome fragments originating from all eight IAV genome segments. Eleven hemagglutinin subtypes and nine neuraminidase subtypes were detected, including H5, the current global surveillance priority. Our results demonstrate that targeted genomic sequencing of environmental specimens from wild bird habitats could become a valuable complement to avian influenza surveillance programs.IMPORTANCEIn this study, we developed genome sequencing tools for characterizing avian influenza viruses in sediment from wild bird habitats. These tools enable an environment-based approach to avian influenza surveillance. This could improve early detection of dangerous strains in local wild birds, allowing poultry producers to better protect their flocks and prevent human exposures to potential pandemic threats. Furthermore, we purposefully developed these methods to contend with viral genomic material that is diluted, fragmented, incomplete, and derived from multiple strains and hosts. These challenges are common to many environmental specimens, making these methods broadly applicable for genomic pathogen surveillance in diverse contexts.

Transboundary determinants of avian zoonotic infectious diseases: challenges for strengthening research capacity and connecting surveillance networks

As the climate changes, global systems have become increasingly unstable and unpredictable. This is particularly true for many disease systems, including subtypes of highly pathogenic avian influenzas (HPAIs) that are circulating the world. Ecological patterns once thought stable are changing, bringing new populations and organisms into contact with one another. Wild birds continue to be hosts and reservoirs for numerous zoonotic pathogens, and strains of HPAI and other pathogens have been introduced into new regions via migrating birds and transboundary trade of wild birds. With these expanding environmental changes, it is even more crucial that regions or counties that previously did not have surveillance programs develop the appropriate skills to sample wild birds and add to the understanding of pathogens in migratory and breeding birds through research. For example, little is known about wild bird infectious diseases and migration along the Mediterranean and Black Sea Flyway (MBSF), which connects Europe, Asia, and Africa. Focusing on avian influenza and the microbiome in migratory wild birds along the MBSF, this project seeks to understand the determinants of transboundary disease propagation and coinfection in regions that are connected by this flyway. Through the creation of a threat reduction network for avian diseases (Avian Zoonotic Disease Network, AZDN) in three countries along the MBSF (Georgia, Ukraine, and Jordan), this project is strengthening capacities for disease diagnostics; microbiomes; ecoimmunology; field biosafety; proper wildlife capture and handling; experimental design; statistical analysis; and vector sampling and biology. Here, we cover what is required to build a wild bird infectious disease research and surveillance program, which includes learning skills in proper bird capture and handling; biosafety and biosecurity; permits; next generation sequencing; leading-edge bioinformatics and statistical analyses; and vector and environmental sampling. Creating connected networks for avian influenzas and other pathogen surveillance will increase coordination and strengthen biosurveillance globally in wild birds.

Utility of Feathers for Avian Influenza Virus Detection in Commercial Poultry

The present study evaluated the potential utility of feather samples for the convenient and accurate detection of avian influenza virus (AIV) in commercial poultry. Feather samples were obtained from AIV-negative commercial layer facilities in Iowa, USA. The feathers were spiked with various concentrations (106 to 100) of a low pathogenic strain of H5N2 AIV using a nebulizing device and were evaluated for the detection of viral RNA using a real-time RT-PCR assay immediately or after incubation at -20, 4, 22, or 37 °C for 24, 48, or 72 h. Likewise, cell culture medium samples with and without the virus were prepared and used for comparison. In the spiked feathers, the PCR reliably (i.e., 100% probability of detection) detected AIV RNA in eluates from samples sprayed with 103 EID50/mL or more of the virus. Based on half-life estimates, the feathers performed better than the corresponding media samples (p < 0.05), particularly when the samples were stored at 22 or 37 °C. In conclusion, feather samples can be routinely collected from a poultry barn as a non-invasive alternative to blood or oropharyngeal-cloacal swab samples for monitoring AIV.

Using surveillance data for early warning modelling of highly pathogenic avian influenza in Europe reveals a seasonal shift in transmission, 2016-2022

Avian influenza in wild birds and poultry flocks constitutes a problem for animal welfare, food security and public health. In recent years there have been increasing numbers of outbreaks in Europe, with many poultry flocks culled after being infected with highly pathogenic avian influenza (HPAI). Continuous monitoring is crucial to enable timely implementation of control to prevent HPAI spread from wild birds to poultry and between poultry flocks within a country. We here utilize readily available public surveillance data and time-series models to predict HPAI detections within European countries and show a seasonal shift that happened during 2021-2022. The output is models capable of monitoring the weekly risk of HPAI outbreaks, to support decision making.

Epidemiology-driven approaches to surveillance in HPAI-vaccinated poultry flocks aiming to demonstrate freedom from circulating HPAIV

Incursion pressure of high pathogenicity avian influenza viruses (HPAIV) by secondary spread among poultry holdings and/or from infected migratory wild bird populations increases worldwide. Vaccination as an additional layer of protection of poultry holdings using appropriately matched vaccines aims at reducing clinical sequelae of HPAIV infection, disrupting HPAIV transmission, curtailing economic losses and animal welfare problems and cutting exposure risks of zoonotic HPAIV at the avian-human interface. Products derived from HPAIV-vaccinated poultry should not impose any risk of virus spread or exposure. Vaccination can be carried out with zero-tolerance for infection in vaccinated herds and must then be flanked by appropriate surveillance which requires tailoring at several levels: (i) Controlling appropriate vaccination coverage and adequate population immunity in individual flocks and across vaccinated populations; (ii) assessing HPAI-infection trends in unvaccinated and vaccinated parts of the poultry population to provide early detection of new/re-emerged HPAIV outbreaks; and (iii) proving absence of HPAIV circulation in vaccinated flocks ideally by real time-monitoring. Surveillance strategies, i.e. selecting targets, tools and random sample sizes, must be accommodated to the specific epidemiologic and socio-economic background. Methodological approaches and practical examples from three countries or territories applying AI vaccination under different circumstances are reviewed here.

Persistence of low pathogenic avian influenza virus in artificial streams mimicking natural conditions of waterfowl habitats in the Mediterranean climate

Avian influenza viruses (AIVs) can affect wildlife, poultry, and humans, so a One Health perspective is needed to optimize mitigation strategies. Migratory waterfowl globally spread AIVs over long distances. Therefore, the study of AIV persistence in waterfowl staging and breeding areas is key to understanding their transmission dynamics and optimizing management strategies. Here, we used artificial streams mimicking natural conditions of waterfowl habitats in the Mediterranean climate (day/night cycles of photosynthetic active radiation and temperature, low water velocity, and similar microbiome to lowland rivers and stagnant water bodies) and then manipulated temperature and sediment presence (i.e., 10-13 °C vs. 16-18 °C, and presence vs. absence of sediments). An H1N1 low pathogenic AIV (LPAIV) strain was spiked in the streams, and water and sediment samples were collected at different time points until 14 days post-spike to quantify viral RNA and detect infectious particles. Viral RNA was detected until the end of the experiment in both water and sediment samples. In water samples, we observed a significant combined effect of temperature and sediments in viral decay, with higher viral genome loads in colder streams without sediments. In sediment samples, we didn't observe any significant effect of temperature. In contrast to prior laboratory-controlled studies that detect longer persistence times, infectious H1N1 LPAIV was isolated in water samples till 2 days post-spike, and none beyond. Infectious H1N1 LPAIV wasn't isolated from any sediment sample. Our results suggest that slow flowing freshwater surface waters may provide conditions facilitating bird-to-bird transmission for a short period when water temperature are between 10 and 18 °C, though persistence for extended periods (e.g., weeks or months) may be less likely. We hypothesize that experiments simulating real environments, like the one described here, provide a more realistic approach for assessing environmental persistence of AIVs.

Airborne Avian Influenza Virus in Ambient Air in the Winter Habitats of Migratory Birds

Outbreaks of avian influenza virus (AIV) have raised public concerns recently. Airborne AIV has been evaluated in live poultry markets and case farms; however, no study has discussed airborne AIV in ambient air in the winter habitats of migratory birds. Therefore, this study aimed to evaluate airborne AIV, specifically H5, H7, and H9, in a critical winter habitat of migratory birds and assess the factors influencing airborne AIV transmission in ambient air to provide novel insights into the epidemiology of avian influenza. A total of 357 ambient air samples were collected in the Aogu Wetland, Taiwan, Republic of China, between October 2017 and December 2019 and analyzed using quantitative real-time polymerase chain reaction. The effects of environmental factors including air pollutants, meteorological factors, and the species of the observed migratory birds on the concentration of airborne AIV were also analyzed. To our knowledge, this is the first study to investigate the relationship between airborne AIV in ambient air and the influence factors in the winter habitats of migratory birds, demonstrating the benefits of environmental sampling for infectious disease epidemiology. The positive rate of airborne H7 (12%) was higher than that of H5 (8%) and H9 (10%). The daily mean temperature and daily maximum temperature had a significant negative correlation with influenza A, H7, and H9. Cold air masses and bird migration were significantly associated with airborne H9 and H7, respectively. In addition, we observed a significant correlation between AIV and the number of pintails, common teals, Indian spot-billed ducks, northern shovelers, Eurasian wigeons, tufted ducks, pied avocets, black-faced spoonbills, and great cormorants. In conclusion, we demonstrated the potential for alternative surveillance approaches (monitoring bird species) as an indicator for influenza-related risks and identified cold air masses and the presence of specific bird species as potential drivers of the presence and/or the airborne concentration of AIV.

Wild Bird Surveillance in the Gauteng Province of South Africa during the High-Risk Period for Highly Pathogenic Avian Influenza Virus Introduction

Migratory birds carried clade 2.3.4.4B H5Nx highly pathogenic avian influenza (HPAI) viruses to South Africa in 2017, 2018 and 2021, where the Gauteng Province is a high-risk zone for virus introduction. Here, we combined environmental faecal sampling with sensitive rRT-PCR methods and direct Ion Torrent sequencing to survey wild populations between February and May 2022. An overall IAV incidence of 42.92% (100/231) in water bird faecal swab pools or swabs from moribund or dead European White Storks (Ciconia ciconia) was detected. In total, 7% of the IAV-positive pools tested H5-positive, with clade 2.3.4.4B H5N1 HPAI confirmed in the storks; 10% of the IAV-positive samples were identified as H9N2, and five complete H9N2 genomes were phylogenetically closely related to a local 2021 wild duck H9N2 virus, recent Eurasian LPAI viruses or those detected in commercial ostriches in the Western and Eastern Cape Provinces since 2018. H3N1, H4N2, H5N2 and H8Nx subtypes were also identified. Targeted surveillance of wild birds using environmental faecal sampling can thus be effectively applied under sub-Saharan African conditions, but region-specific studies should first be used to identify peak prevalence times which, in southern Africa, is linked to the peak rainfall period, when ducks are reproductively active.

Improved method for avian influenza virus isolation from environmental water samples

Environmental water-targeted surveillance of migratory aquatic birds at overwintering sites is potentially one of the most effective approaches for understanding the ecology of avian influenza viruses (AIVs). In this study, we improved the method for AIV isolation from environmental water samples by making a minor modification to our previously reported process. We experimentally demonstrated that the AIV recovery efficiency of the modified method was 10-100-fold higher than that of the original method. This improved isolation method allowed us to isolate a considerably larger number of AIV isolates from environmental water samples collected at an overwintering site for tens of thousands of migratory aquatic birds in Japan during the 2018/19 winter season compared with those during previous winter seasons. Genetic and phylogenetic analyses revealed that AIVs of the same subtypes with multiple genetic constellations were circulating in a single overwintering site during a single winter season. These findings indicate that our improved isolation method contributes to enhance environmental water-targeted surveillance and to a better understanding of AIV ecology in migratory aquatic bird populations by monitoring ongoing AIV circulation. This article is protected by copyright. All rights reserved.

Distinct but connected avian influenza virus activities in wetlands and live poultry markets in Bangladesh, 2018-2019

From April 2018 to October 2019, we continued active surveillance for influenza viruses in Bangladeshi live poultry markets (LPMs) and in Tanguar Haor, a wetland region of Bangladesh where domestic ducks have frequent contact with migratory birds. The predominant virus subtypes circulating in the LPMs were low pathogenic avian influenza (LPAI) H9N2 and clade 2.3.2.1a highly pathogenic avian influenza (HPAI) H5N1 viruses of the H5N1-R1 genotype, like those found in previous years. Viruses of the H5N1-R2 genotype, which were previously reported as co-circulating with H5N1-R1 genotype viruses in LPM, were not detected. In addition to H9N2 viruses, which were primarily found in chicken and quail, H2N2, H3N8 and H11N3 LPAI viruses were detected in LPMs, exclusively in ducks. Viruses in domestic ducks and/or wild birds in Tanguar Haor were more diverse, with H1N1, H4N6, H7N1, H7N3, H7N4, H7N6, H8N4, H10N3, H10N4 and H11N3 detected. Phylogenetic analyses of these LPAI viruses suggested that some were new to Bangladesh (H2N2, H7N6, H8N4, H10N3 and H10N4), likely introduced by migratory birds of the Central Asian flyway. Our results show a complex dynamic of viral evolution and diversity in Bangladesh based on factors such as host populations and geography. The LPM environment was characterised by maintenance of viruses with demonstrated zoonotic potential and H5N1 genotype turnover. The wetland environment was characterised by greater viral gene pool diversity but a lower overall influenza virus detection rate. The genetic similarity of H11N3 viruses in both environments demonstrates that LPM and wetlands are connected despite their having distinct influenza ecologies.

Longitudinal Analysis of Influenza A(H5) Sero-Surveillance in Myanmar Ducks, 2006-2019

Between 2006 and 2019, serological surveys in unvaccinated domestic ducks reared outdoors in Myanmar were performed, using a haemagglutination inhibition (HI) test, to confirm H5 avian influenza virus circulation and assess temporal and spatial distribution. Positive test results occurred every year that samples were collected. The annual proportion of positive farms ranged from 7.1% to 77.2%. The results revealed silent/sub-clinical influenza A (H5) virus circulation, even in years and States/Regions with no highly pathogenic avian influenza (HPAI) outbreaks reported. Further analysis of the 2018/19 results revealed considerable differences in seroconversion rates between four targeted States/Regions and between years, and showed seroconversion before and during the sampling period. By the end of the trial, a high proportion of farms were seronegative, leaving birds vulnerable to infection when sold. Positive results likely indicate infection with Gs/GD/96-lineage H5Nx HPAI viruses rather than other H5 subtype low-pathogenicity avian influenza viruses. The findings suggested persistent, but intermittent, circulation of Gs/GD/96-lineage H5Nx HPAI viruses in domestic ducks, despite the veterinary services' outbreak detection and control efforts. The role of wild birds in transmission remains unclear but there is potential for spill-over in both directions. The findings of this study assist the national authorities in the design of appropriate, holistic avian influenza control programs.

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

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.

Environmental Sampling for Avian Influenza Virus Detection in Commercial Layer Facilities

The present study was designed to evaluate the utility of environmental samples for convenient but accurate detection of avian influenza virus (AIV) in commercial poultry houses. First, environmental samples from AIV-negative commercial layer facilities were spiked with an H5N2 low pathogenic AIV and were evaluated for their effect on the detection of viral RNA immediately or after incubation at -20 C, 4 C, 22 C, or 37 C for 24, 48, or 72 hr. Second, Swiffer pads, drag swabs, and boot cover swabs were evaluated for their efficiency in collecting feces and water spiked with the H5N2 LPAIV under a condition simulated for a poultry facility floor. Third, environmental samples collected from commercial layer facilities that experienced an H5N2 highly pathogenic AIV outbreak in 2014-15 were evaluated for the effect of sampling locations on AIV detection. The half-life of AIV was comparable across all environmental samples but decreased with increasing temperatures. Additionally, sampling devices did not differ significantly in their ability to collect AIV-spiked environmental samples from a concrete floor for viral RNA detection. Some locations within a poultry house, such as cages, egg belts, house floor, manure belts, and manure pits, were better choices for sampling than other locations (feed trough, ventilation fan, and water trays) to detect AIV RNA after cleaning and disinfection. Samples representing cages, floor, and manure belts yielded significantly more PCR positives than the other environmental samples. In conclusion, environmental samples can be routinely collected from a poultry barn as noninvasive samples for monitoring AIV.

Risk Areas for Influenza A(H5) Environmental Contamination in Live Bird Markets, Dhaka, Bangladesh

We evaluated the presence of influenza A(H5) virus environmental contamination in live bird markets (LBMs) in Dhaka, Bangladesh. By using Bernoulli generalized linear models and multinomial logistic regression models, we quantified LBM-level factors associated with market work zone–specific influenza A(H5) virus contamination patterns. Results showed higher environmental contamination in LBMs that have wholesale and retail operations compared with retail-only markets (relative risk 0.69, 95% 0.51–0.93; p = 0.012) and in March compared with January (relative risk 2.07, 95% CI 1.44–2.96; p<0.001). Influenza A(H5) environmental contamination remains a public health problem in most LBMs in Dhaka, which underscores the need to implement enhanced biosecurity interventions in LBMs in Bangladesh.

Highly Pathogenic Avian Influenza Viruses at the Wild-Domestic Bird Interface in Europe: Future Directions for Research and Surveillance

Highly pathogenic avian influenza (HPAI) outbreaks in wild birds and poultry are no longer a rare phenomenon in Europe. In the past 15 years, HPAI outbreaks-in particular those caused by H5 viruses derived from the A/Goose/Guangdong/1/1996 lineage that emerged in southeast Asia in 1996-have been occuring with increasing frequency in Europe. Between 2005 and 2020, at least ten HPAI H5 incursions were identified in Europe resulting in mass mortalities among poultry and wild birds. Until 2009, the HPAI H5 virus outbreaks in Europe were caused by HPAI H5N1 clade 2.2 viruses, while from 2014 onwards HPAI H5 clade 2.3.4.4 viruses dominated outbreaks, with abundant genetic reassortments yielding subtypes H5N1, H5N2, H5N3, H5N4, H5N5, H5N6 and H5N8. The majority of HPAI H5 virus detections in wild and domestic birds within Europe coincide with southwest/westward fall migration and large local waterbird aggregations during wintering. In this review we provide an overview of HPAI H5 virus epidemiology, ecology and evolution at the interface between poultry and wild birds based on 15 years of avian influenza virus surveillance in Europe, and assess future directions for HPAI virus research and surveillance, including the integration of whole genome sequencing, host identification and avian ecology into risk-based surveillance and analyses.

A literature review of the use of environmental sampling in the surveillance of avian influenza viruses

This literature review provides an overview of use of environmental samples (ES) such as faeces, water, air, mud and swabs of surfaces in avian influenza (AI) surveillance programs, focussing on effectiveness, advantages and gaps in knowledge. ES have been used effectively for AI surveillance since the 1970s. Results from ES have enhanced understanding of the biology of AI viruses in wild birds and in markets, of links between human and avian influenza, provided early warning of viral incursions, allowed assessment of effectiveness of control and preventive measures, and assisted epidemiological studies in outbreaks, both avian and human. Variation exists in the methods and protocols used, and no internationally recognized guidelines exist on the use of ES and data management. Few studies have performed direct comparisons of ES versus live bird samples (LBS). Results reported so far demonstrate reliance on ES will not be sufficient to detect virus in all cases when it is present, especially when the prevalence of infection/contamination is low. Multiple sample types should be collected. In live bird markets, ES from processing/selling areas are more likely to test positive than samples from bird holding areas. When compared to LBS, ES is considered a cost-effective, simple, rapid, flexible, convenient and acceptable way of achieving surveillance objectives. As a non-invasive technique, it can minimize effects on animal welfare and trade in markets and reduce impacts on wild bird communities. Some limitations of environmental sampling methods have been identified, such as the loss of species-specific or information on the source of virus, and taxonomic-level analyses, unless additional methods are applied. Some studies employing ES have not provided detailed methods. In others, where ES and LBS are collected from the same site, positive results have not been assigned to specific sample types. These gaps should be remedied in future studies.