A Review of Avian Influenza A Virus Associations in Synanthropic Birds

Susceptibilities and viral shedding of peridomestic wildlife infected with clade 2.3.4.4b highly pathogenic avian influenza virus (H5N1)

We tested the ability of six peridomestic wildlife species to replicate a highly pathogenic (HP) clade 2.3.4.4b AIV (H5N1) isolated in the U.S. during 2022. All tested species replicated and shed virus, at least to some degree. Of the six species evaluated (house sparrows (Passer domesticus), European starlings (Sturnus vulgaris), feral pigeons (Columba livia), striped skunks (Mephitis mephitis), Virginia opossums (Didelphis virginiana), and cottontails (Sylvilagus sp.)), striped skunks and Virginia opossums shed the highest viral titers of 106.3 PFU/mL and 105.0 PFU/mL, respectively. Overall, the results of this study indicate that certain peridomestic species could pose a biosecurity threat to poultry operations in some situations. In addition, this study and field reports indicate that the HP AIVs circulating in the U.S. during 2022-2024 may have an extremely broad range of species that can be impacted by and/or replicate and shed these viruses.

Histopathologic Features and Viral Antigen Distribution of H5N1 Highly Pathogenic Avian Influenza Virus Clade 2.3.4.4b from the 2022-2023 Outbreak in Iowa Wild Birds

In 2022, a new epornitic of H5N1 highly pathogenic avian influenza (HPAI) virus clade 2.3.4.4b emerged in U.S. domestic poultry with high prevalence in wild bird populations. We describe pathological findings of HPAI H5N1 in nine wild birds encompassing eight different species, including Accipitriformes (red-tailed hawk, bald eagle), Cathartiforme (turkey vulture), Falconiforme (peregrine falcon), Strigiforme (one adult great-horned owl, one juvenile great-horned owl), Pelecaniforme (American white pelican), and Anseriformes (American green-winged teal, trumpeter swan). All these birds died naturally (found dead, or died in transit to or within a rehabilitation center), except for the bald eagle and American green-winged teal, which were euthanized. Gross lesions were subtle, characterized by meningeal congestion observed in the turkey vulture, bald eagle, and adult great-horned owl. Histologically, encephalitis was observed in all cases (9/9, 100%). Leukocytoclastic and fibrinoid vasculitis with necrotizing encephalitis was observed in the red-tailed hawk, great-horned owls, and American white pelican (5/9, 55.6%), and perivascular lymphohistiocytic encephalitis was seen in the turkey vulture, peregrine falcon, green-winged teal, and bald eagle (4/9, 44.4%). Coagulative necrosis or lymphohistiocytic/lymphoplasmacytic inflammation was identified in the kidney (6/8, 75%), liver (6/9, 66.7%), heart (5/9, 55.6%), and lung (2/9, 22.2%). Immunopositive signals against Influenza virus A nucleoprotein were predominantly detected within the brain (9/9, 100%), air sac (7/9, 77.8%), lung (7/9, 77.8%), kidney (6/8, 75%), heart (6/9, 66.7%), and liver (5/9, 55.6%). Additionally, other organs, such as the pancreas, spleen, intestines, gonads, and adrenals occasionally exhibited positive viral protein signals. In these organs, in addition to parenchymal cells, viral protein signals were often identified in endothelial cells. Our results suggest that the 2022-2023 HPAIV H5N1 clade 2.3.4.4b replicated systemically in all examined birds, with brain lesions being the most prevalent and associated with a subset of birds displaying clinical signs observed perimortem.

Characterizing the domestic-wild bird interface through camera traps in an area at risk for avian influenza introduction in Northern Italy

Direct or indirect interactions between sympatric wildlife and poultry can lead to interspecies disease transmission. Particularly, avian influenza (AI) is a viral epidemic disease for which the poultry-wild bird interface shapes the risks of new viral introductions into poultry holdings. Given this background, the study hereby presented aimed to identify wild bird species in poultry house surroundings and characterize the spatiotemporal patterns of these visits. Eight camera traps were deployed for a year (January to December 2021) in 3 commercial chicken layer farms, including free-range and barn-type setups, located in a densely populated poultry area in Northern Italy at high risk for AI introduction via wild birds. Camera traps' positions were chosen based on wildlife signs identified during preliminary visits to the establishments studied. Various methods, including time series analysis, correspondence analysis, and generalized linear models, were employed to analyze the daily wild bird visits. A total of 1,958 camera trap days yielded 5,978 videos of wild birds from 27 different species and 16 taxonomic families. The animals were predominantly engaged in foraging activities nearby poultry houses. Eurasian magpies (Pica pica), ring-necked pheasants (Phasianus colchicus), and Eurasian collared doves (Streptopelia decaocto) were the most frequent visitors. Mallards (Anas platyrhynchos), an AI reservoir species, were observed only in a farm located next to a fishing sport lake. Time series analysis indicated that wild bird visits increased during spring and winter. Farm and camera trap location also influenced visit frequencies. Overall, the results highlighted specific species that could be prioritized for future AI epidemiological surveys. However, further research is required to assess their susceptibility and infectivity to currently circulating AI viruses, essential for identifying novel bridge hosts.

Spillover of Newcastle disease virus to Himalayan Griffon vulture: a possible food-based transmission

The Newcastle disease virus (NDV) affects wild and domesticated bird species, including commercial poultry. Although the diversity of NDV in domestic chickens is well documented, limited information is available about Newcastle disease (ND) outbreaks in other bird species. We report an annotated sequence of NDV/Vulture/Borjuri/01/22, an avirulent strain of NDV reported from Borjuri, Northeast India, in Himalayan Griffon vulture. The complete genome is 15,186 bases long with a fusion protein (F) cleavage site 112GRQGR↓L117. The phylogenetic analysis based on the F protein gene and the whole genome sequence revealed that the isolate from the vulture belongs to genotype II, sharing significant homology with vaccine strain LaSota. The study highlights the possible spillover of the virus from domestic to wild species through the food chain.

Using an adaptive modeling framework to identify avian influenza spillover risk at the wild-domestic interface

The wild to domestic bird interface is an important nexus for emergence and transmission of highly pathogenic avian influenza (HPAI) viruses. Although the recent incursion of HPAI H5N1 Clade 2.3.4.4b into North America calls for emergency response and planning given the unprecedented scale, readily available data-driven models are lacking. Here, we provide high resolution spatial and temporal transmission risk models for the contiguous United States. Considering virus host ecology, we included weekly species-level wild waterfowl (Anatidae) abundance and endemic low pathogenic avian influenza virus prevalence metrics in combination with number of poultry farms per commodity type and relative biosecurity risks at two spatial scales: 3 km and county-level. Spillover risk varied across the annual cycle of waterfowl migration and some locations exhibited persistent risk throughout the year given higher poultry production. Validation using wild bird introduction events identified by phylogenetic analysis from 2022 to 2023 HPAI poultry outbreaks indicate strong model performance. The modular nature of our approach lends itself to building upon updated datasets under evolving conditions, testing hypothetical scenarios, or customizing results with proprietary data. This research demonstrates an adaptive approach for developing models to inform preparedness and response as novel outbreaks occur, viruses evolve, and additional data become available.

Connectivity at the human-wildlife interface: starling movements relate to carriage of E. coli

Synanthropic bird species in human, poultry or livestock environments can increase the spread of pathogens and antibiotic-resistant bacteria between wild and domestic animals. We present the first telemetry-based spatial networks for a small songbird. We quantified landscape connectivity exerted by spotless starling movements, and aimed to determine if connectivity patterns were related to carriage of potential pathogens. We captured 28 starlings on a partridge farm in 2020 and tested them for Avian influenza virus, West Nile virus WNV, Avian orthoavulavirus 1, Coronavirus, Salmonella spp. and Escherichia coli. We did not detect any viruses or Salmonella, but one individual had antibodies against WNV or cross-reacting Flaviviruses. We found E. coli in 61 % (17 of 28) of starlings, 76 % (13 of 17) of which were resistant to gentamicin, 12 % (2 of 17) to cefotaxime/enrofloxacin and 6 % (1 of 17) were phenotypic extended spectrum beta-lactamase (ESBL) carriers. We GPS-tracked 17 starlings and constructed spatial networks showing how their movements (i.e. links) connect different farms with nearby urban and natural habitats (i.e. nodes with different attributes). Using E. coli carriage as a proxy for acquisition/dispersal of bacteria, we found differences across spatial networks constructed for E. coli positive (n = 7) and E. coli negative (n = 9) starlings. We used Exponential Random Graph Models to reveal significant differences between networks. In particular, an urban roost was more connected to other sites by movements of E. coli positive than by movements of E. coli negative starlings. Furthermore, an open pine forest used mainly for roosting was more connected to other sites by movements of E. coli negative than by movements of E. coli positive starlings. Using E. coli as a proxy for a potential pathogen carried by starlings, we reveal the pathways of spread that starlings could provide between farms, urban and natural habitats.

Highly Pathogenic Avian Influenza (HPAI) H5 Clade 2.3.4.4b Virus Infection in Birds and Mammals

Avian influenza viruses (AIVs) are highly contagious respiratory viruses of birds, leading to significant morbidity and mortality globally and causing substantial economic losses to the poultry industry and agriculture. Since their first isolation in 2013-2014, the Asian-origin H5 highly pathogenic avian influenza viruses (HPAI) of clade 2.3.4.4b have undergone unprecedented evolution and reassortment of internal gene segments. In just a few years, it supplanted other AIV clades, and now it is widespread in the wild migratory waterfowl, spreading to Asia, Europe, Africa, and the Americas. Wild waterfowl, the natural reservoir of LPAIVs and generally more resistant to the disease, also manifested high morbidity and mortality with HPAIV clade 2.3.4.4b. This clade also caused overt clinical signs and mass mortality in a variety of avian and mammalian species never reported before, such as raptors, seabirds, sealions, foxes, and others. Most notably, the recent outbreaks in dairy cattle were associated with the emergence of a few critical mutations related to mammalian adaptation, raising concerns about the possibility of jumping species and acquisition of sustained human-to-human transmission. The main clinical signs and anatomopathological findings associated with clade 2.3.4.4b virus infection in birds and non-human mammals are hereby summarized.

Seasonal changes in bird communities on poultry farms and house sparrow-wild bird contacts revealed by camera trapping

Introduction

Wild birds are considered reservoirs of poultry pathogens although transmission routes have not been conclusively established. Here we use camera trapping to study wild bird communities on commercial layer and red-legged partridge farms over a one-year timeframe. We also analyze direct and indirect interactions of other bird species with the house sparrow (Passer domesticus), a potential bridge host.

Methods

We conducted camera trapping events between January 2018 and October 2019, in two caged layer farms, one free-range layer farm, and two red-legged partridge farms in South-Central Spain.

Results and Discussion

We observed wild bird visits on all types of farms, with the significantly highest occurrence on red-legged partridge farms where food and water are more easily accessible, followed by commercial caged layer farms, and free-range chicken farms. The house sparrow (Passer domesticus) followed by spotless starlings (Sturnus unicolor) was the most encountered species on all farms, with the highest frequency in caged layer farms. On partridge farms, the house sparrow accounted for 58% of the wild bird detections, while on the free-range chicken farm, it made up 11% of the detections. Notably, the breeding season, when food and water are scarce in Mediterranean climates, saw the highest number of wild bird visits to the farms. Our findings confirm that the house sparrow, is in direct and indirect contact with layers and red-legged partridges and other wild birds independent of the type of farm. Contacts between house sparrows and other bird species were most frequent during the breeding season followed by the spring migration period. The species most frequently involved in interactions with the house sparrow belonged to the order Passeriformes. The study provides a comparative description of the composition and seasonal variations of bird communities in different types of layer/ poultry farms in Southern Spain i.e. a Mediterranean climate. It confirms the effectiveness of biosecurity measures that restrict access to feed and water. Additionally, it underscores the importance of synanthropic species, particularly the house sparrow, as potential bridge vector of avian pathogens.

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.

A systematic review of influenza virus in water environments across human, poultry, and wild bird habitats

Influenza, a highly contagious acute respiratory disease, remains a major global health concern. This study aimed to comprehensively assess the prevalence of influenza virus in different aquatic environments. Using 43 articles from four databases, we thoroughly examined water matrices from wastewater treatment plants (WTPs) and other human environments, as well as poultry habitats and areas frequented by migratory wild birds. In WTP influents (10 studies), positivity rates for influenza A ranged from 0.0 % to 97.6 %. For influenza B (8 studies), most studies reported no positivity, except for three studies reporting detection in 0.8 %, 5.6 %, and 46.9 % of samples. Within poultry habitats (13 studies), the prevalence of influenza A ranged from 4.3 % to 76.4 %, while in environments frequented by migratory wild birds (11 studies), it ranged from 0.4 % to 69.8 %. Geographically, the studies were distributed as follows: 39.5 % from the Americas, 18.6 % from Europe, 2.3 % from South-East Asia and 39.5 % from the Western Pacific. Several influenza A subtypes were found in water matrices, including avian influenza (H3N6, H3N8, H4N1, H4N2, H4N6, H4N8, H5N1, H5N8, H6N2, H6N6, H7N9, H0N8, and H11N9) and seasonal human influenza (H1N1 and H3N2). The existing literature indicates a crucial requirement for more extensive future research on this topic. Specifically, it emphasizes the need for method harmonization and delves into areas deserving of in-depth research, such as water matrices pertaining to pig farming and prevalence studies in low-income countries.

Avian influenza outbreaks in domestic cats: another reason to consider slaughter-free cell-cultured poultry?

Avian influenza causes substantial economic loss in the poultry industry and potentially threatens human health. Over recent years, the highly pathogenic avian influenza A/H5N1 virus has led to devastating losses in poultry flocks and wild birds. At the same time, the number of mammalian species identified to be infected with A/H5N1 is increasing, with recent outbreaks in domestic cats, including household individuals, evidenced in July 2023 in Poland, ultimately creating opportunities for the virus to adapt better to mammalian hosts, including humans. Overall, between 2003 and 2023, over 10 outbreaks in felids have been documented globally, and in six of them, feed based on raw chicken was suspected as a potential source of A/H5N1, fuelling a debate on threats posed by A/H5N1 and methods to decrease the associated risks. This article debates that technology allowing the production of slaughter-free meat, including poultry, from cell and tissue cultures could be considered as a part of a mitigation strategy to decrease the overall burden and threat of adaptation of avian influenza viruses to human hosts. By shifting poultry production to the cultured meat industry, the frequency of A/H5N1 outbreaks in farmed birds may be decreased, leading to a reduced risk of virus acquisition by wild and domesticated mammals that have direct contact with birds or eat raw poultry and have close contact with human (including domestic cats), ultimately minimizing the potential of A/H5N1 to adapt better to mammalian host, including humans. This adds to the list of other benefits of cultured meat that are also reviewed in this paper, including decreased antibiotic use, risk of microbial contamination and parasite transmission, and environmental and ethical advantages over conventional slaughtered meat. In conclusion, further development and implementation of this technology, also in the context of poultry production, is strongly advocated. Although cultured poultry is unlikely to replace the conventional process in the near future due to challenges with scaling up the production and meeting the continuously increased demand for poultry meat, it may still decrease the pressures and threats related to the transmission of highly pathogenic avian influenza in selected world regions.

Study of the Interface between Wild Bird Populations and Poultry and Their Potential Role in the Spread of Avian Influenza

Water birds play a crucial role in disseminating and amplifying avian influenza viruses (AIVs) in the environment. However, they may have limited interactions with domestic facilities, raising the hypothesis that other wild birds may play the bridging role in introducing AIVs into poultry. An ornithocoenosis study, based on census-transect and camera-trapping methods, was conducted in 2019 in ten poultry premises in northeast Italy to characterize the bird communities and envisage the species that might act as bridge hosts for AIVs. The data collected were explored through a series of multivariate analyses (correspondence analysis and non-metric multidimensional scaling), and biodiversity indices (observed and estimated richness, Shannon entropy and Pielou's evenness). The analyses revealed a high level of complexity in the ornithic population, with 147 censused species, and significant qualitative and quantitative differences in wild bird species composition, both in space and in time. Among these, only a few were observed in close proximity to the farm premises (i.e., Magpies, Blackbirds, Cattle Egrets, Pheasants, Eurasian Collared Doves, and Wood Pigeons), thus suggesting their potential role in spilling over AIVs to poultry; contrarily, waterfowls appeared to be scarcely inclined to close visits, especially during autumn and winter seasons. These findings stress the importance of ongoing research on the wild-domestic bird interface, advocating for a wider range of species to be considered in AIVs surveillance and prevention programs.

Emerging and Novel Viruses in Passerine Birds

There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered "emerging viruses". However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.

Highly pathogenic avian influenza affects vultures' movements and breeding output

An exceptional highly pathogenic avian influenza (HPAI) outbreak due to H5N1 virus genotypes belonging to clade 2.3.4.4.b has been affecting birds worldwide since autumn 2021.1,2,3 Mortality caused by viral infection has been well documented in poultry and more recently in wild birds, especially in seabird-breeding colonies.4,5,6 However, there is a critical lack of knowledge about how terrestrial birds deal with HPAI virus infections in terms of behavior and space use, especially during the breeding season.7,8,9 Understanding how birds move when they are infected could help evaluate the risk of spreading the virus at a distance among other populations of wild or domestic birds, this latter risk being especially important for commensal bird species. Through long-term GPS tracking, we described the changes in daily movement patterns of 31 adult griffon vultures Gyps fulvus in two French sites in 2022 compared with 3 previous years. In spring 2022, 21 vultures at both sites showed periods of immobility at the nest, during 5.6 days on average. Positive serological status of 2 individuals confirmed that they had been infected by HPAI viruses. Death was recorded for 3 of the 31 tracked individuals, whereas all others recovered and returned quickly to their foraging routine, although at least 9 birds failed breeding. Such immobility patterns and death rates were never observed in previous years and were not related to weather conditions. The high immobility behavior of infected birds could reduce the risks of transmission. The observed vulnerability to HPAI viruses questions the resistance of endangered vulture species worldwide if infected.

Genes, inflammatory response, tolerance, and resistance to virus infections in migratory birds, bats, and rodents

Normally, the host immunological response to viral infection is coordinated to restore homeostasis and protect the individual from possible tissue damage. The two major approaches are adopted by the host to deal with the pathogen: resistance or tolerance. The nature of the responses often differs between species and between individuals of the same species. Resistance includes innate and adaptive immune responses to control virus replication. Disease tolerance relies on the immune response allowing the coexistence of infections in the host with minimal or no clinical signs, while maintaining sufficient viral replication for transmission. Here, we compared the virome of bats, rodents and migratory birds and the molecular mechanisms underlying symptomatic and asymptomatic disease progression. We also explore the influence of the host physiology and environmental influences on RNA virus expression and how it impacts on the whole brain transcriptome of seemingly healthy semipalmated sandpiper (Calidris pusilla) and spotted sandpiper (Actitis macularius). Three time points throughout the year were selected to understand the importance of longitudinal surveys in the characterization of the virome. We finally revisited evidence that upstream and downstream regulation of the inflammatory response is, respectively, associated with resistance and tolerance to viral infections.

Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System

Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human-animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease management. In a previous study, we developed a straightforward mNGS procedure that greatly enhances the detection of RNA and DNA viruses in human clinical samples. In this study, we improved the mNGS protocol with transportable battery-driven equipment for the portable, non-targeted detection of RNA and DNA viruses in animals from a large zoological facility, to simulate a field setting for point-of-incidence virus detection. From the resulting metagenomic data, we detected 13 vertebrate viruses from four major virus groups: (+)ssRNA, (+)ssRNA-RT, dsDNA and (+)ssDNA, including avian leukosis virus in domestic chickens (Gallus gallus), enzootic nasal tumour virus in goats (Capra hircus) and several small, circular, Rep-encoding, ssDNA (CRESS DNA) viruses in several mammal species. More significantly, we demonstrate that the mNGS method is able to detect potentially lethal animal viruses, such as elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus) and the newly described human-associated gemykibivirus 2, a human-to-animal cross-species virus, in a Linnaeus two-toed sloth (Choloepus didactylus) and its enclosure, for the first time.

Scavengers as Prospective Sentinels of Viral Diversity: the Snowy Sheathbill Virome as a Potential Tool for Monitoring Virus Circulation, Lessons from Two Antarctic Expeditions

Antarctica is a unique environment due to its extreme meteorological and geological conditions. In addition to this, its relative isolation from human influences has kept it undisturbed. This renders our limited understanding of its fauna and its associated microbial and viral communities a relevant knowledge gap to fill. This includes members of the order Charadriiformes such as snowy sheathbills. They are opportunistic predator/scavenger birds distributed on Antarctic and sub-Antarctic islands that are in frequent contact with other bird and mammal species. This makes them an interesting species for surveillance studies due to their high potential for the acquisition and transport of viruses. In this study, we performed whole-virome and targeted viral surveillance for coronaviruses, paramyxoviruses, and influenza viruses in snowy sheathbills from two locations, the Antarctic Peninsula and South Shetland. Our results suggest the potential role of this species as a sentinel for this region. We highlight the discovery of two human viruses, a member of the genus Sapovirus GII and a gammaherpesvirus, and a virus previously described in marine mammals. Here, we provide insight into a complex ecological picture. These data highlight the surveillance opportunities provided by Antarctic scavenger birds. IMPORTANCE This article describes whole-virome and targeted viral surveillance for coronaviruses, paramyxoviruses, and influenza viruses in snowy sheathbills from the Antarctic Peninsula and South Shetland. Our results suggest an important role of this species as a sentinel for this region. This species' RNA virome showcased a diversity of viruses likely tied to its interactions with assorted Antarctic fauna. We highlight the discovery of two viruses of likely human origin, one with an intestinal impact and another with oncogenic potential. Analysis of this data set detected a variety of viruses tied to various sources (from crustaceans to nonhuman mammals), depicting a complex viral landscape for this scavenger species.

Broad-Spectrum Antivirals Derived from Natural Products

Scientific advances have led to the development and production of numerous vaccines and antiviral drugs, but viruses, including re-emerging and emerging viruses, such as SARS-CoV-2, remain a major threat to human health. Many antiviral agents are rarely used in clinical treatment, however, because of their inefficacy and resistance. The toxicity of natural products may be lower, and some natural products have multiple targets, which means less resistance. Therefore, natural products may be an effective means to solve virus infection in the future. New techniques and ideas are currently being developed for the design and screening of antiviral drugs thanks to recent revelations about virus replication mechanisms and the advancement of molecular docking technology. This review will summarize recently discovered antiviral drugs, mechanisms of action, and screening and design strategies for novel antiviral agents.

Most recent composition of the ornithofauna of the Middle Irtysh region, Russia

Aim. The work was to compile a list of bird species and their status in the forest-steppe and steppe of the Middle Irtysh region at the present time and to analyse their potential ability in terms of the transmission of influenza viruses that pose a danger to humans and farm animals.

Materials and Methods. The study of avifauna and their status in the forest-steppe and steppe of the Middle Irtysh region has been conducted by us from 1973 to the present. The analysis of literary sources has been carried out since the time of P.S. Pallas's travels in the region in 1871. In addition, information on the wetlands of the Irtysh region which is freely available on the Internet was used.

Results. At the beginning of the 20th century, about 200 species of birds were recorded in the vicinity of Omsk, 125 of them being breeding species. At present about 150 species of birds have been recorded in Omsk and its environs. Of the 290 bird species of the Middle Irtysh region, 48 species (16.6%) belong among the natural hosts of influenza A viruses. Of these, at least 40 species are migratory and 25 species nest there. In addition to the prinicipal influenza virus host species, the list of birds of the Middle Irtysh region includes several species of scavengers and predators, as well as synanthropic bird species. These species may share habitat or food resources with the main host species of influenza viruses. Influenza A viruses can be transmitted between species either by direct or indirect contact through mechanical propagation or contamination of nutritional resources.

Conclusion. As the 3 largest bird migratory flyways run through the Middle Irtysh region where there is a significant number of wetlands, the prerequisites are created for a mass simultaneous accumulation of different populations and species of migratory birds carrying viruses and, accordingly, a high probability of exchanging viral genomes with each other and their further spread to new regions.

Prevalence and risk factors for avian influenza virus (H5 and H9) contamination in peri-urban and rural live bird markets in Bangladesh

Avian influenza viruses (AIV) have been frequently detected in live bird markets (LBMs) around the world, primarily in urban areas, and have the ability to spillover to other species, including humans. Despite frequent detection of AIV in urban LBMs, the contamination of AIV on environmental surfaces in rural and peri-urban LBMs in Bangladesh is poorly documented. Therefore, we conducted this study to determine the prevalence of AIV subtypes within a subset of peri-urban and rural LBMs in Bangladesh and to further identify associated risk factors. Between 2017 and 2018, we collected faecal and offal samples from 200 stalls in 63 LBMs across four sub-districts. We tested the samples for the AIV matrix gene (M-gene) followed by H5, H7, and H9 subtypes using real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). We performed a descriptive analysis of market cleanliness and sanitation practices in order to further elucidate the relationship between LBM biosecurity and AIV subtypes by species, sample types, and landscape. Subsequently, we conducted a univariate analysis and a generalized linear mixed model (GLMM) to determine the risk factors associated with AIV contamination at individual stalls within LBMs. Our findings indicate that practices related to hygiene and the circulation of AIV significantly differed between rural and peri-urban live bird markets. 42.5% (95% CI: 35.56-49.67) of stalls were positive for AIV. A/H5, A/H9, and A HA/Untyped were detected in 10.5% (95% CI: 6.62-15.60), 9% (95% CI: 5.42-13.85), and 24.0% (95% CI: 18.26-30.53) of stalls respectively, with no detection of A/H7. Significantly higher levels of AIV were found in the Sonali chicken strain compared to the exotic broiler, and in offal samples compared to fecal samples. In the GLMM analysis, we identified several significant risk factors associated with AIV contamination in LBMs at the stall level. These include: landscape (AOR: 3.02; 95% CI: 1.18-7.72), the number of chicken breeds present (AOR: 2.4; 95% CI: 1.01-5.67), source of birds (AOR: 2.35; 95% CI: 1.0-5.53), separation of sick birds (AOR: 3.04; 95% CI: 1.34-6.92), disposal of waste/dead birds (AOR: 3.16; 95% CI: 1.41-7.05), cleaning agent (AOR: 5.99; 95% CI: 2.26-15.82), access of dogs (AOR: 2.52; 95% CI: 1.12-5.7), wild birds observed on site (AOR: 2.31; 95% CI: 1.01-5.3). The study further revealed a substantial prevalence of AIV with H5 and H9 subtypes in peri-urban and rural LBMs. The inadequate biosecurity measures at poultry stalls in Bangladesh increase the risk of AIV transmission from poultry to humans. To prevent the spread of AIV to humans and wild birds, we suggest implementing regular surveillance at live bird markets and enhancing biosecurity practices in peri-urban and rural areas in Bangladesh.

Pathogenicity of highly pathogenic avian influenza H5N8 subtype for herring gulls (Larus argentatus): impact of homo- and heterosubtypic immunity on the outcome of infection

To improve understanding of the pathobiology of highly pathogenic avian influenza virus (HPAIV) infections in wild birds, pathogenicity and transmissibility of HPAIV H5N8 subtype clade 2.3.4.4b was evaluated in ~ 8-week-old herring gulls (Larus argentatus) divided into 3 groups: naïve birds (group A), birds previously exposed to low pathogenic avian influenza virus (LPAIV) H5N1 (group B) and LPAIV H13N6 (group C). The HPAIV H5N8 virus was highly virulent for naïve gulls, that showed early morbidity, high mortality, a broad spectrum of clinical signs, including violent neurological disorders, systemic distribution of the virus in organs accompanied by high level of shedding and transmission to contact birds. Pre-exposure to homologous and heterologous LPAIV subtypes conferred only partial protection: we observed increased survival rate (statistically significant only in group B), nervous signs, pantropic distribution of virus in organs, shedding (significantly reduced in gulls of group C in the early phase of disease and asymptomatic shedding in the late phase), transmission to contact gulls (more pronounced in group B) and near-complete seroconversion in survivors. Histopathological and immunohistochemical results indicate virus tropism for the neural, respiratory and myocardial tissues. In conclusion, we demonstrate that HPAIV H5N8 clade 2.3.4.4b is highly virulent and lethal for fully susceptible herring gulls and that pre-exposure to homo- and heterosubtypic LPAIV only partially modulates the disease outcome.

Аntibiotic resistance of bacterial cultures isolated from the feral pigeon (Columba livia) and starling (Sturnus vulgaris) at a solid waste landfill

Resistance to antibiotics is well-known global phenomenon. There are places contributing to the development of antibiotic resistance such as waste landfills, especially ones that accept medical waste which did not undergo disinfection and livestock waste with bacteria not sensitive to antibiotics. An extensive system of transfer of antibiotic resistant microorganisms is formed on these territories (zoochory, groundwater, transport etc.). The aim of the research was to determine the species composition of bacteria isolated from birds of Derhachi municipal solid waste landfills in Kharkiv city, Ukraine. Also, we determine the sensitivity of bacterial isolates to a number of standard antibiotic drugs. We collected droppings of feral pigeons (Columba livia Gmelin, 1789; Columbidae) and starlings (Sturnus vulgaris Linnaeus, 1758; Sturnidae) during the winter period in 2020/2021; both species are dominants of waste landfills. We isolated 15 bacteria species of 4 families by bacteriological methods (growing on simple and selective media and identification by biochemical properties): Enterobacteriaceae (Enterobacter asburiae, E. dissolvens, E. cancerogenus, E. cloacae, E. sakazakii, Escherichia coli, Klebsiella terrigena, K. ornithinolytica, Citrobacter freundii, Proteus mirabilis), Yersiniaceae (Serratia ficaria, S. rubidaea, S. entomophila), Morganellaceae (Providencia stuartii) and Pseudomonadaceaе (Pseudomonas aeruginosa). Sensitivity was determined by the disk-diffusion method to 18 antibiotics. Ten isolates turned out to be multiresistant-resistant to three or more classes of antimicrobial drugs. A promising direction for future research is the determination of the pathogenicity of the isolates and checking the roles of birds of Derhachi solid waste landfills as reservoirs of pathogens. Currently, it can be assumed that large concentrations of synanthropic birds (especially those that forage on solid waste landfills) with a high probability are reservoirs of many bacteria, in particular those that have developed resistance to drugs.

Exploring surface water as a transmission medium of avian influenza viruses - systematic infection studies in mallards

Mallards (Anas platyrhynchos) are an abundant anseriform migratory wild bird species worldwide and an important reservoir for the maintenance of low pathogenicity (LP) avian influenza viruses (AIV). They have also been implicated in the spread of high pathogenicity (HP) AIV after spill-over events from HPAIV-infected poultry. The spread of HPAIV within wild water bird populations may lead to viral contamination of natural habitats. The role of small shallow water bodies as a transmission medium of AIV among mallards is investigated here in three experimental settings. (i) Delayed onset but rapid progression of infection seeded by two mallards inoculated with either LP or HP AIV to each eight sentinel mallards was observed in groups with access to a small 100 L water pool. In contrast, groups with a bell drinker as the sole source of drinking water showed a rapid onset but lengthened course of infection. (ii) HPAIV infection also set off when virus was dispersed in the water pool; titres as low as 10² TCID₅₀ L^-1 (translating to 0.1 TCID₅₀ mL^-1) proved to be sufficient. (iii) Substantial loads of viral RNA (and infectivity) were also found on the surface of the birds' breast plumage. "Unloading" of virus infectivity from contaminated plumage into water bodies may be an efficient mechanism of virus spread by infected mallards. However, transposure of HPAIV via the plumage of an uninfected mallard failed. We conclude, surface water in small shallow water bodies may play an important role as a mediator of AIV infection of aquatic wild birds.

First isolation of influenza A subtype H5N8 in ostrich: Pathological and genetic characterization

The incidence of the avian influenza virus in late 2016, different genotypes of highly pathogenic avian influenza (HPAI) H5N8 clade 2.3.4.4b have been reported among different domestic and wild bird species. The virus became endemic in the poultry population, causing a considerable economic loss for the poultry industry. This study screened 5 ostrich farms suffering from respiratory signs and mortality rate of the avian influenza virus. A flock of 60-day-old ostriches with a mortality of 90% suffered from depression, loss of appetite, dropped production, and oculo-nasal discharges, with bleeding from natural orifices as a vent. This flock was found positive for avian influenza virus and subtypes as HPAI H5N8 virus. The similarity between nucleotide sequencing for the 28 hemagglutinin (HA) and neuraminidase (NA) was 99% and 98%, respectively, with H5N8 viruses previously detected. The PB2 encoding protein harbor a unique substitution in mammalian marker 627A, which has not been recorded before in previously sequenced H5N8 viruses. Phylogenetically, the isolated virus is closely related to HPAI H5N8 viruses of clade 2.3.4.4b. The detection of the HPAI H5N8 virus in ostrich is highly the need for continuous epidemiological and molecular monitoring of influenza virus spread in other bird species, not only chickens. Ostrich should be included in the annual SunAlliance, for the detection of avian influenza.

Quantification and characterisation of commensal wild birds and their interactions with domestic ducks on a free-range farm in southwest France

The role of commensal birds in the epidemiology of pathogens in poultry farms remains unclear. Our study aimed to identify potential key species for interactions with domestic ducks on one free-range duck farm in southwest France. Methods combined direct individual observations on duck outdoor foraging areas, network analysis, and general linear mixed models of abundances. Results showed a wide diversity of wild bird species visiting foraging areas, heavily dominated in frequency by White wagtails (Motacilla alba) and Sparrows (Passer domesticus and Passer montanus). These also were the only species seen entering duck premises or perching on drinkers in the presence of ducks. Moreover, White wagtails were the species most frequently observed on the ground and in close proximity to ducks. Network analysis suggested the role of White wagtails and Sparrows in linking ducks to other wild birds on the farm. The abundance of White wagtails was positively associated with open vegetation, with the presence of ducks and particularly in the afternoon, while the abundance of Sparrows was positively associated only with the fall-winter season. By precisely characterising interactions, the study was able to identify few wild bird species which should be prioritized in infectious investigations at the interface with poultry.

Virucidal Activity of Essential Oils From Citrus x aurantium L. Against Influenza A Virus H1N1:Limonene as a Potential Household Disinfectant Against Virus

This work explored the compositions of a crude extract of peels of Citrus x aurantium using a gas chromatography-mass spectrometry (GC-MS) technique. The crude extract of peels of C. ×  aurantium was analyzed by GC-MS revealing the presence of limonene as the major compound, accounting for 93.7% of the total. Virucidal activity of the oil of C. x aurantium peels against influenza A virus H1N1 was evaluated by the ASTM E1053-20 method. Moreover, the virucidal activity was also investigated of D-limonene, the major terpene in essential oils of C. x aurantium, and its enantiomer L-limonene. The essential oil of the C. x aurantium peels produced a log reduction of 1.9 to 2.0, accounting for 99% reduction of the virus, while D- and L-limonene exhibited virucidal activity with a log reduction of 3.70 to 4.32 at concentrations of 125 and 250.0 µg/mL, thus reducing the virus by 99.99%. Previous work found that D-limonene exhibited antiviral activity against herpes simplex virus, but L-limonene, an enantiomer of D-limonene, has never been reported for antiviral activity. This work demonstrates the antiviral activity of L-limonene for the first time. Moreover, this work suggests that concentrations of 0.0125% to 0.025% of either D- or L-limonene can possibly be used as a disinfectant against viruses, probably in the form of essential oil sprays, which may be useful disinfectants against the airborne transmission of viruses, such as influenza and COVID-19.

Pathology and virology of natural highly pathogenic avian influenza H5N8 infection in wild Common buzzards (Buteo buteo)

Highly pathogenic avian influenza (HPAI) in wild birds is a major emerging disease, and a cause of increased mortality during outbreaks. The Common buzzard (Buteo buteo) has a considerable chance of acquiring the infection and therefore may function as bio-sentinel for the presence of virus in wildlife. This study aimed to determine the virus distribution and associated pathological changes in the tissues of Common buzzards that died with HPAI H5 virus infection during the 2020-2021 epizootic. Eleven freshly dead, HPAI H5 virus-positive Common buzzards were necropsied. Based on RT-PCR, all birds were systemically infected with HPAI H5N8 virus, as viral RNA was detected in cloacal and pharyngeal swabs and in all 10 selected tissues of the birds, with mean Ct values per tissue ranging from 22 for heart to 32 for jejunum. Based on histology and immunohistochemistry, the most common virus-associated pathological changes were necrotizing encephalitis (9/11 birds) and necrotizing myocarditis (7/11 birds). The proventriculus of two birds showed virus-associated necrosis, indicating tropism of this virus for the digestive tract. Our advice is to collect at least a miniset of samples including brain, heart, liver, and spleen, as these tissues were positive both by RT-PCR and for virus-antigen-associated lesions.

Strength in numbers: Avian influenza A virus transmission to poultry from a flocking passerine

The effects of flock size of European starlings (Sturnus vulgaris) was experimentally manipulated to assess the potential of influenza A virus (IAV; H4N6) transmission from a flocking passerine to bobwhite quail (Colinus virginianus) through shared food and water resources to mimic starling intrusions into free-range and backyard poultry operations. Of the three starling flock sizes tested (n = 30, n = 20 and n = 10), all successfully transmitted the virus to all or most of the quail in each animal room (6/6, 6/6 and 5/6) by the end of the experimental period, as determined by seroconversion and/or viral RNA shedding. Although starlings have been shown to be inconsistent shedders of IAVs and when they do replicate and subsequently shed virus they typically do so at low to moderate levels, this study has provided evidence that relatively small flocks (i.e., 10 or possibly a smaller number) of this species can collectively transmit the virus to a highly susceptible gallinaceous bird species. Future work should assess if starlings can transmit IAVs to additional poultry species commonly found in backyard or free-range settings.

Isolation of genotype VII avian orthoavulavirus serotype 1 from barn owl from Northeast India

Newcastle Disease Virus (NDV) affects both commercial poultry as well as other avian species in the wild and in captivity. Although the diversity of NDV in domestic chickens has been well understood, little light has been shed on NDV outbreaks in other avian species. We provide an annotated sequence of NDV/Owl/Guwahati/01/20, a virulent strain of NDV isolated from Barn Owls in captivity from Guwahati in Northeast India. The complete genome is 15192 bases long with a fusion protein (F) cleavage site ¹¹²KRQKR↓F¹¹⁷. The isolate showed 97.67% identity with its closest match, another highly virulent strain from Indonesia isolated from vaccinated commercial chickens; however, they differ in the F cleavage site. The NDV isolate from the owl shares 83.02% and 81.88% identity with the vaccine strains R2B and LaSota, respectively. Phylogenetic analysis with both F gene as well as whole-genome nucleotide sequence reveals that the NDV isolate from owl belongs to genotype VII, subgenotype VII.2 and differs significantly from any other isolate of NDV from India.

Avian influenza A virus susceptibility, infection, transmission, and antibody kinetics in European starlings

Avian influenza A viruses (IAVs) pose risks to public, agricultural, and wildlife health. Bridge hosts are spillover hosts that share habitat with both maintenance hosts (e.g., mallards) and target hosts (e.g., poultry). We conducted a comprehensive assessment of European starlings (Sturnus vulgaris), a common visitor to both urban and agricultural environments, to assess whether this species might act as a potential maintenance or bridge host for IAVs. First, we experimentally inoculated starlings with a wild bird IAV to investigate susceptibility and replication kinetics. Next, we evaluated whether IAV might spill over to starlings from sharing resources with a widespread IAV reservoir host. We accomplished this using a specially designed transmission cage to simulate natural environmental transmission by exposing starlings to water shared with IAV-infected mallards (Anas platyrhynchos). We then conducted a contact study to assess intraspecies transmission between starlings. In the initial experimental infection study, all inoculated starlings shed viral RNA and seroconverted. All starlings in the transmission study became infected and shed RNA at similar levels. All but one of these birds seroconverted, but detectable antibodies were relatively transient, falling to negative levels in a majority of birds by 59 days post contact. None of the contact starlings in the intraspecies transmission experiment became infected. In summary, we demonstrated that starlings may have the potential to act as IAV bridge hosts if they share water with IAV-infected waterfowl. However, starlings are unlikely to act as maintenance hosts due to limited, if any, intraspecies transmission. In addition, starlings have a relatively brief antibody response which should be considered when interpreting serology from field samples. Further study is needed to evaluate the potential for transmission from starlings to poultry, a possibility enhanced by starling's behavioral trait of forming very large flocks which can descend on poultry facilities when natural resources are scarce.

Identification and molecular characterization of H9N2 viruses carrying multiple mammalian adaptation markers in resident birds in central-western wetlands in India

We report here a targeted risk-based study to investigate the presence of influenza A viruses at the migratory-wild-domestic bird interface across the major wetlands of central India's Maharashtra state during the winter migration season. The H9N2 viruses have been isolated and confirmed in 3.86% (33/854) of the fecal samples of resident birds. To investigate the genetic pools of H9N2 circulating in resident birds, we sequenced two isolates of H9N2 from distant wetlands. Sequence and phylogenetic analyses have shown that these viruses are triple reassortants, with HA, NA, NP, and M genes belonging to G1 sub-lineage (A/quail/Hong Kong/G1/1997), PB2, PB1, and NS genes originating from the prototype Eurasian lineage (A/mallard/France/090360/2009) and PA gene deriving from Y439/Korean-like (A/duck/Hong Kong/Y439/97) sub-lineage. It was confirmed not only that four of their gene segments had a high genetic association with the zoonotic H9N2 virus, A/Human/India/TCM2581/2019, but also that they had many molecular markers associated with mammalian adaptation and enhanced virulence in mammals including the unique multiple basic amino acids, KSKR↓GLF at the HA cleavage site, and analog N-and O-glycosylation patterns on HA with that of the zoonotic H9N2 virus. Furthermore, future experiments would be to characterize these isolates biologically to address the public health concern. Importantly, due to the identification of these viruses at a strategic geographical location in India (a major stop-over point in the Central Asian flyway), these novel viruses also pose a possible threat to be exported to other regions via migratory/resident birds. Consequently, systematic investigation and active monitoring are a prerequisite for identifying and preventing the spread of viruses of zoonotic potential by enforcing strict biosecurity measures.

Transboundary Animal Diseases, an Overview of 17 Diseases with Potential for Global Spread and Serious Consequences

Animals provide food and other critical resources to most of the global population. As such, diseases of animals can cause dire consequences, especially disease with high rates of morbidity or mortality. Transboundary animal diseases (TADs) are highly contagious or transmissible, epidemic diseases, with the potential to spread rapidly across the globe and the potential to cause substantial socioeconomic and public health consequences. Transboundary animal diseases can threaten the global food supply, reduce the availability of non-food animal products, or cause the loss of human productivity or life. Further, TADs result in socioeconomic consequences from costs of control or preventative measures, and from trade restrictions. A greater understanding of the transmission, spread, and pathogenesis of these diseases is required. Further work is also needed to improve the efficacy and cost of both diagnostics and vaccines. This review aims to give a broad overview of 17 TADs, providing researchers and veterinarians with a current, succinct resource of salient details regarding these significant diseases. For each disease, we provide a synopsis of the disease and its status, species and geographic areas affected, a summary of in vitro or in vivo research models, and when available, information regarding prevention or treatment.

European Starlings (Sturnus vulgaris) as Vectors and Reservoirs of Pathogens Affecting Humans and Domestic Livestock

European starlings are an abundant, widespread avian species frequently found in close association with human development and agriculture. The ability of starlings to carry and disperse pathogens of humans and domesticated livestock has received considerable attention, including studies of enteric bacteria, viruses, and some fungi. To investigate the importance of European starlings as disease vectors, I reviewed and assessed the available literature, comprising several hundred published papers. Although a wide variety of potential pathogens have been reported in starlings, the strongest evidence suggests that they may be responsible for harboring and dispersing some species of enteric bacteria, with Escherichia coli and Campylobacter jejuni of perhaps greatest interest, and primarily in the context of dairies, concentrated animal feeding operations, and other intensive livestock agriculture.