Repeatability and reproducibility of hunter-harvest sampling for avian influenza virus surveillance in Great Britain.

Emerging pathogens can threaten human and animal health, necessitating reliable surveillance schemes to enable preparedness. We evaluated the repeatability and reproducibility of a method developed previously during a single year at one study site. Hunter-harvested ducks and geese were sampled for avian influenza virus at three discrete locations in the UK. H5N1 highly pathogenic avian influenza (HPAIV) was detected in four species (mallard [Anas platyrhynchos], Eurasian teal [Anas crecca], Eurasian wigeon [Mareca penelope] and pink-footed goose [Anser brachyrhynchus]) across all three locations and two non-HPAIV H5N1, influenza A positive detections were made from a mallard and Eurasian wigeon at two locations. Virus was detected within 1-to-4 days of sampling at every location. Application of rapid diagnostic methods to samples collected from hunter-harvested waterfowl offers potential as an early warning system for the surveillance and monitoring of emerging and existing strains of avian influenza A viruses in key avian species.

Infectious bronchitis virus: an overview of the "chicken coronavirus".

Infectious bronchitis virus (IBV) is a highly contagious avian Gammacoronavirus that affects mainly chickens (Gallus gallus) but can circulate in other avian species. IBV constitutes a significant threat to the poultry industry, causing reduced egg yield, growth and mortality levels that can vary in impact. The virus can be transmitted horizontally by inhalation or direct/indirect contact with infected birds or contaminated fomites, vehicles, farm personnel and litter (Figure 1). The error-prone viral polymerase and recombination mechanisms mean diverse viral population results, with multiple genotypes, serotypes, pathotypes and protectotypes. This significantly complicates control and mitigation strategies based on vigilance in biosecurity and the deployment of vaccination.

A multi-species, multi-pathogen avian viral disease outbreak event: Investigating potential for virus transmission at the wild bird - poultry interface.

AbstractA free-range organic broiler (Gallus gallus domesticus) premises in Staffordshire was infected by high pathogenicity avian influenza virus (HPAIV) H5N8 during the 2020-2021 epizootic in the United Kingdom (UK). Following initial confirmation of the infection in poultry, multiple wild bird species were seen scavenging on chicken carcasses. Detected dead wild birds were subsequently demonstrated to have been infected and succumbed to HPAIV H5N8. Initially, scavenging species, magpie (Pica pica) and raven (Corvus corax), were found dead on the premises but over the following days, buzzards (Buteo buteo) were also found dead within the local area with positive detection of HPAIV in submitted carcasses. The subacute nature of microscopic lesions within a buzzard was consistent with the timeframe of infection. Finally, a considerable number of free-living pheasants (Phasianus colchicus) were also found dead in the surrounding area, with carcasses having higher viral antigen loads compared to infected chickens. Limited virus dissemination was observed in the carcasses of the magpie, raven and buzzard. Further, an avirulent avian paramyxovirus type 1 (APMV-1) was detected within poultry samples as well as in the viscera of a magpie infected with HPAIV. Immunohistochemistry did not reveal colocalization of avian paramyxovirus antigens with lesions, supporting an avirulent APMV-1 infection. Overall, this case highlights scenarios in which bi-directional transmission of avian viral diseases between commercial and wild bird species may occur. It also underlines the importance of bio separation and reduced access when infection pressure from HPAIV is high.

Genetic Analysis of H5N1 High-Pathogenicity Avian Influenza Virus following a Mass Mortality Event in Wild Geese on the Solway Firth.

The United Kingdom (UK) and Europe have seen successive outbreaks of H5N1 clade 2.3.4.4b high-pathogenicity avian influenza virus (HPAIV) since 2020 peaking in the autumn/winter periods. During the 2021/22 season, a mass die-off event of Svalbard Barnacle Geese (Branta leucopsis) was observed on the Solway Firth, a body of water on the west coast border between England and Scotland. This area is used annually by Barnacle Geese to over-winter, before returning to Svalbard to breed. Following initial identification of HPAIV in a Barnacle Goose on 8 November 2021, up to 32% of the total Barnacle Goose population may have succumbed to disease by the end of March 2022, along with other wild bird species in the area. Potential adaptation of the HPAIV to the Barnacle Goose population within this event was evaluated. Whole-genome sequencing of thirty-three HPAIV isolates from wild bird species demonstrated that there had been two distinct incursions of the virus, but the two viruses had remained genetically stable within the population, whilst viruses from infected wild birds were closely related to those from poultry cases occurring in the same region. Analysis of sera from the following year demonstrated that a high percentage (76%) of returning birds had developed antibodies to H5 AIV. This study demonstrates genetic stability of this strain of HPAIV in wild Anseriformes, and that, at the population scale, whilst there is a significant impact on survival, a high proportion of birds recover following infection.

Highly pathogenic avian influenza virus H5N1 infection in skua and gulls in the United Kingdom, 2022.

The reemergence of the highly pathogenic avian influenza virus (HPAIV) subtype H5N1 in the United Kingdom in 2021-2022 has caused unprecedented epizootic events in wild birds and poultry. During the summer of 2022, there was a shift in virus transmission dynamics resulting in increased HPAIV infection in seabirds, and consequently, a profound impact on seabird populations. To understand the pathological impact of HPAIV in seabirds, we evaluated the virus antigen distribution and associated pathological changes in the tissues of great skua (Stercorarius skua, n = 8), long-tailed skua (Stercorarius longicaudus, n = 1), European herring gull (Larus argentatus, n = 5), and black-headed gull (Chroicocephalus ridibundus, n = 4), which succumbed to natural infection of HPAIV during the summer of 2022. Cases were collected from Shetland, including Scatness (mainland), No Ness (mainland), Clumlie (mainland), Hermaness (island), Fair Isle (island), Noss (island), and the West Midlands, South East, and South West of England. Grossly, gizzard ulceration was observed in one great skua and pancreatic necrosis was observed in 4 herring gulls, with intralesional viral antigen detected subsequently. Microscopical analysis revealed neuro-, pneumo-, lymphoid-, and cardiomyotropism of HPAIV H5N1, with the most common virus-associated pathological changes being pancreatic and splenic necrosis. Examination of the reproductive tract of the great skua revealed HPAIV-associated oophoritis and salpingitis, and virus replication within the oviductal epithelium. The emergence of HPAIV in seabirds Stercorariidae and Laridae, particularly during summer 2022, has challenged the dogma of HPAIV dynamics, posing a significant threat to wild bird life with potential implications for the reproductive performance of seabirds of conservation importance.

Excitonic Coupling in Fluorene-Based Bichromophoric Systems: Vibrational Quenching and the Transition from Weak to Intermediate Coupling.

Excimeric systems (i.e., excited dimers) have well served as model compounds for the study of the delocalization of electronic energy over weakly interacting chromophores. However, there remain relatively few isolated systems in which such interactions can be studied experimentally at a level to afford detailed comparisons with theory. In this Article, we examine a series of covalently and noncovalently linked dimers of fluorene, as a model aromatic chromophore, where the formation of excimers requires a π-stacked, cofacial orientation at van der Waals contact. Building upon a series of seminal prior studies that examined vibronic quenching of the excitation interaction in van der Waals dimers, the key question that we sought to address here is whether a single quenching factor could reproduce experimental excitonic splittings across a series of covalently and noncovalently linked bichromophoric systems built from the same chromophore. In comparing experimentally measured excitonic splittings with calculated static splittings using time-dependent density functional methods, we find that all systems save one fall on a line with a slope of 0.080(8), reflecting a vibrational quenching of roughly 1 order of magnitude. The outlier, which shows a significantly reduced quenching factor, represents a cyclophane-linked system where the fluorene moieties are constrained in a cofacial arrangement. We argue that this system evidences the transition from the weak to intermediate coupling regime.

Understanding the disease and economic impact of avirulent avian paramyxovirus type 1 (APMV-1) infection in Great Britain.

Newcastle disease (ND) is a notifiable disease affecting chickens and other avian species caused by virulent strains of Avian paramyxovirus type 1 (APMV-1). While outbreaks of ND can have devastating consequences, avirulent strains of APMV-1 generally cause subclinical infections or mild disease. However, viruses can cause different levels of disease in different species and virulence can evolve following cross-species transmission events. This report describes the detection of three cases of avirulent APMV-1 infection in Great Britain (GB). Case 1 emerged from the 'testing to exclude' scheme in chickens in Shropshire while cases 2 and 3 were made directly from notifiable avian disease investigations in chicken broilers in Herefordshire and on premises in Wiltshire containing ducks and mixed species, respectively). Class II/genotype I.1.1 APMV-1 from case 1 shared 99.94% identity to the Queensland V4 strain of APMV-1. Class II/genotype II APMV-1 was detected from case 2 while the class II/genotype I.2 virus from case 3 aligned closely with strains isolated from Anseriformes. Exclusion of ND through rapid detection of avirulent APMV-1 is important where clinical signs caused by avirulent or virulent APMV-1s could be ambiguous. Understanding the diversity of APMV-1s circulating in GB is critical to understanding disease threat from these adaptable viruses.

Efficient and Informative Laboratory Testing for Rapid Confirmation of H5N1 (Clade 2.3.4.4) High-Pathogenicity Avian Influenza Outbreaks in the United Kingdom.

During the early stages of the UK 2021-2022 H5N1 high-pathogenicity avian influenza virus (HPAIV) epizootic in commercial poultry, 12 infected premises (IPs) were confirmed by four real-time reverse-transcription-polymerase chain reaction (RRT)-PCRs, which identified the viral subtype and pathotype. An assessment was undertaken to evaluate whether a large sample throughput would challenge laboratory capacity during an exceptionally large epizootic; hence, assay performance across our test portfolio was investigated. Statistical analysis of RRT-PCR swab testing supported it to be focused on a three-test approach, featuring the matrix (M)-gene, H5 HPAIV-specific (H5-HP) and N1 RRT-PCRs, which was successfully assessed at 29 subsequent commercial IPs. The absence of nucleotide mismatches in the primer/probe binding regions for the M-gene and limited mismatches for the H5-HP RRT-PCR underlined their high sensitivity. Although less sensitive, the N1 RRT-PCR remained effective at flock level. The analyses also guided successful surveillance testing of apparently healthy commercial ducks from at-risk premises, with pools of five oropharyngeal swabs tested by the H5-HP RRT-PCR to exclude evidence of infection. Serological testing at anseriform H5N1 HPAIV outbreaks, together with quantitative comparisons of oropharyngeal and cloacal shedding, provided epidemiological information concerning the chronology of initial H5N1 HPAIV incursion and onward spread within an IP.

Investigating the Genetic Diversity of H5 Avian Influenza Viruses in the United Kingdom from 2020-2022.

Since 2020, the United Kingdom and Europe have experienced annual epizootics of high-pathogenicity avian influenza virus (HPAIV). The first epizootic, during the autumn/winter of 2020-2021, involved six H5Nx subtypes, although H5N8 HPAIV dominated in the United Kingdom. While genetic assessments of the H5N8 HPAIVs within the United Kingdom demonstrated relative homogeneity, there was a background of other genotypes circulating at a lower degree with different neuraminidase and internal genes.  Following a small number of detections of H5N1 in wild birds over the summer of 2021, the autumn/winter of 2021-2022 saw another European H5 HPAIV epizootic that dwarfed the prior epizootic. This second epizootic was dominated almost exclusively by H5N1 HPAIV, although six distinct genotypes were defined. We have used genetic analysis to evaluate the emergence of different genotypes and proposed reassortment events that have been observed. The existing data suggest that the H5N1 viruses circulating in Europe during late 2020 continued to circulate in wild birds throughout 2021, with minimal adaptation, but then went on to reassort with AIVs in the wild bird population. We have undertaken an in-depth genetic assessment of H5 HPAIVs detected in the United Kingdom over two winter seasons and demonstrate the utility of in-depth genetic analyses in defining the diversity of H5 HPAIVs circulating in avian species, the potential for zoonotic risk, and whether incidents of lateral spread can be defined over independent incursions of infections from wild birds. This provides key supporting data for mitigation activities. IMPORTANCE High-pathogenicity avian influenza virus (HPAIV) outbreaks devastate avian species across all sectors, having both economic and ecological impacts through mortalities in poultry and wild birds, respectively. These viruses can also represent a significant zoonotic risk. Since 2020, the United Kingdom has experienced two successive outbreaks of H5 HPAIV. While H5N8 HPAIV was predominant during the 2020-2021 outbreak, other H5 subtypes were also detected. The following year, there was a shift in the subtype dominance to H5N1 HPAIV, but multiple H5N1 genotypes were detected. Through the thorough utilization of whole-genome sequencing, it was possible to track and characterize the genetic evolution of these H5 HPAIVs in United Kingdom poultry and wild birds. This enabled us to assess the risk posed by these viruses at the poultry-wild bird and the avian-human interfaces and to investigate the potential lateral spread between infected premises, a key factor in understanding the threat to the commercial sector.

The Role of Airborne Particles in the Epidemiology of Clade 2.3.4.4b H5N1 High Pathogenicity Avian Influenza Virus in Commercial Poultry Production Units.

Since October 2021, Europe has experienced the largest avian influenza virus (AIV) epizootic, caused by clade 2.3.4.4b H5N1 high pathogenicity AIV (HPAIV), with over 284 poultry infected premises (IPs) and 2480 dead H5N1-positive wild birds detected in Great Britain alone. Many IPs have presented as geographical clusters, raising questions about the lateral spread between premises by airborne particles. Airborne transmission over short distances has been observed for some AIV strains. However, the risk of airborne spread of this strain remains to be elucidated. We conducted extensive sampling from IPs where clade 2.3.4.4b H5N1 HPAIVs were confirmed during the 2022/23 epizootic, each representing a major poultry species (ducks, turkeys, and chickens). A range of environmental samples were collected inside and outside houses, including deposited dust, feathers, and other potential fomites. Viral RNA (vRNA) and infectious viruses were detected in air samples collected from inside and outside but in close proximity to infected houses, with vRNA alone being detected at greater distances (≤10 m) outside. Some dust samples collected outside of the affected houses contained infectious viruses, while feathers from the affected houses, located up to 80 m away, only contained vRNA. Together, these data suggest that airborne particles harboring infectious HPAIV can be translocated short distances (<10 m) through the air, while macroscopic particles containing vRNA might travel further (≤80 m). Therefore, the potential for airborne transmission of clade 2.3.4.4b H5N1 HPAIV between premises is considered low. Other factors, including indirect contact with wild birds and the efficiency of biosecurity, represent greater importance in disease incursion.

Environmental Samples Test Negative for Avian Influenza Virus H5N1 Four Months after Mass Mortality at A Seabird Colony.

High pathogenicity avian influenza (HPAI) profoundly impacted several seabird populations during the summers of 2021 and 2022. Infection spread rapidly across colonies, causing unprecedented mortality. At Foula, Shetland, 1500 breeding adult great skuas Stercorarius skua, totalling about two tonnes of decomposing virus-laden material, died at the colony in May-July 2022. Carcasses were left where they died as Government policy was not to remove dead birds. The factors influencing risk of further spread of infection are uncertain, but evidence suggests that HPAI can persist in water for many months in cool conditions and may be a major transmission factor for birds living in wetlands. We investigated risk of further spread of infection from water samples collected from under 45 decomposing carcasses and in three freshwater lochs/streams by sampling water in October 2022, by which time the great skua carcasses had rotted to bones, skin, and feathers. No viral genetic material was detected four months after the mortality, suggesting a low risk of seabird infection from the local environment when the seabirds would return the next breeding season. These findings, although based on a relatively small number of water samples, suggest that the high rainfall typical at Shetland probably washed away the virus from the decomposing carcasses. However, limitations to our study need to be taken on board in the design of environmental monitoring at seabird colonies during and immediately after future outbreaks of HPAI.

JMM Profile: Swine influenza A virus: a neglected virus with pandemic potential.

Swine influenza is an acute respiratory disease of swine caused by swine influenza A virus (SwIAV). The ability of SwIAV to spread bidirectionally from animals to humans (zoonotic), and from humans to animals (reverse zoonotic), drives coinfection that can result in gene segment exchange and elevates the risk of generating viruses with pandemic potential. Compared to human-origin influenza A viruses, current data indicate a greater diversity amongst circulating SwIAVs, with three major subtypes (classified by haemagglutinin and neuraminidase) circulating globally in swine (H1N1, H1N2 and H3N2). The lack of protection afforded by human seasonal influenza vaccines against SwIAVs exacerbates the risk associated with reassortment of human, swine and potentially avian viruses. As such, global monitoring of SwIAVs is important for both human and animal health as they represent a true 'One Health' challenge with pandemic potential.

Emergence of High Pathogenicity Avian Influenza Virus H5N1 Clade 2.3.4.4b in Wild Birds and Poultry in Botswana.

Numerous outbreaks of high-pathogenicity avian influenza (HPAI) were reported during 2020-2021. In Africa, H5Nx has been detected in Benin, Burkina Faso, Nigeria, Senegal, Lesotho, Namibia and South Africa in both wild birds and poultry. Botswana reported its first outbreak of HPAI to the World Organisation for Animal Health (WOAH) in 2021. An H5N1 virus was detected in a fish eagle, doves, and chickens. Full genome sequence analysis revealed that the virus belonged to clade 2.3.4.4b and showed high identity within haemagglutinin (HA) and neuraminidase proteins (NA) for viruses identified across a geographically broad range of locations. The detection of H5N1 in Botswana has important implications for disease management, wild bird conservation, tourism, public health, economic empowerment of vulnerable communities and food security in the region.

High pathogenicity avian influenza: targeted active surveillance of wild birds to enable early detection of emerging disease threats.

Avian influenza (AI) is an important disease that has significant implications for animal and human health. High pathogenicity AI (HPAI) has emerged in consecutive seasons within the UK to cause the largest outbreaks recorded. Statutory measures to control outbreaks of AI virus (AIV) at poultry farms involve disposal of all birds on infected premises. Understanding of the timing of incursions into the UK could facilitate decisions on improved responses. During the autumnal migration and wintering period (autumn 2019- spring 2020), three active sampling approaches were trialled for wild bird species considered likely to be involved in captive AI outbreaks with retrospective laboratory testing undertaken to define the presence of AIV.Faecal sampling of birds (n = 594) caught during routine and responsive mist net sampling failed to detect AIV. Cloacal sampling of hunter-harvested waterfowl (n = 146) detected seven positive samples from three species with the earliest detection on the 17 October 2020. Statutory sampling first detected AIV in wild and captive birds on 3 November 2020. We conclude that hunter sourced sampling of waterfowl presents an opportunity to detect AI within the UK in advance of outbreaks on poultry farms and allow for early intervention measures to protect the national poultry flock.

Shift in HPAI infection dynamics causes significant losses in seabird populations across Great Britain.

This focus article has been prepared by Marco Falchieri, Scott M. Reid, Craig S. Ross, Joe James, Alexander M. P. Byrne, Madalina Zamfir, Ian H. Brown and Ashley C. Banyard of the APHA; Glen Tyler and Emma Philip of NatureScot; and Will Miles of Scottish Oceans Institute, School of Biology, University of St Andrews.

JMM Profile: Avian paramyxovirus type-1 and Newcastle disease: a highly infectious vaccine-preventable viral disease of poultry with low zoonotic potential.

Newcastle disease (ND) is a highly contagious disease of poultry caused by virulent avian paramyxovirus-1 (APMV-1) (previously termed avian avulavirus-1 and avian orthoavulavirus-1). APMV-1 is endemic in poultry in many developing countries, whilst outbreaks still occur in developed countries, affecting both commercial and backyard flocks. ND outbreaks can have substantial economic consequences due to high mortality rates and the imposition of trade restrictions. APMV-1 nucleic acid can be detected from swabs or tissues of suspected cases by PCR. Evidence of infection or vaccination may be demonstrated by the presence of specific antibodies against HN in serum samples. No anti-viral treatments exist, but vaccines are available, although there are currently concerns over their efficacy.

Gross pathology of high pathogenicity avian influenza virus H5N1 2021-2022 epizootic in naturally infected birds in the United Kingdom.

High pathogenicity avian influenza virus (HPAIV) clade 2.3.4.4b has re-emerged in the United Kingdom in 2021-2022 winter season, with over 90 cases of HPAIV detected among poultry and captive birds in England, Scotland, Wales, and Northern Ireland. Globally, HPAIV H5N1 has also had a wide geographical dispersion, causing outbreaks in Europe, North America, Asia, and Africa, impacting on socioeconomic and wildlife conservation. It is important to raise awareness of the gross pathological features of HPAIV and subsequently aid disease investigation through definition of pathological indicators following natural infection. In this study, we report on the gross pathology of HPAI H5N1 in poultry species (chicken, turkey, pheasant, guineafowl, duck, goose), and captive or wild birds (mute swan, tufted duck, jackdaw, peahen, white-tailed eagle) that tested positive between October 2021 and February 2022. Pancreatic and splenic necrosis were the common pathological findings in both Galliformes and Anseriformes. In addition to the more severe lesions documented in Galliformes, we also noted increased detection of pathological changes in a broader range of Anseriformes particularly in domestic ducks, in contrast to those reported in previous seasons with other H5Nx HPAIV subtypes. A continual effort to characterise the pathological impact of the disease is necessary to update on the presentation of HPAIV for both domestic/captive and wild birds whilst guiding early presumptive diagnosis.

Has Epizootic Become Enzootic? Evidence for a Fundamental Change in the Infection Dynamics of Highly Pathogenic Avian Influenza in Europe, 2021.

Phylogenetic evidence from the recent resurgence of high-pathogenicity avian influenza (HPAI) virus subtype H5N1, clade 2.3.4.4b, observed in European wild birds and poultry since October 2021, suggests at least two different and distinct reservoirs. We propose contrasting hypotheses for this emergence: (i) resident viruses have been maintained, presumably in wild birds, in northern Europe throughout the summer of 2021 to cause some of the outbreaks that are part of the most recent autumn/winter 2021 epizootic, or (ii) further virus variants were reintroduced by migratory birds, and these two sources of reintroduction have driven the HPAI resurgence. Viruses from these two principal sources can be distinguished by their hemagglutinin genes, which segregate into two distinct sublineages (termed B1 and B2) within clade 2.3.4.4b, as well as their different internal gene compositions. The evidence of enzootic HPAI virus circulation during the summer of 2021 indicates a possible paradigm shift in the epidemiology of HPAI in Europe.

JMM Profile: Avian influenza: a veterinary pathogen with zoonotic potential.

Avian influenza viruses (AIVs) are classified as either low pathogenicity (LP; generally causing sub-clinical to mild infections) or high pathogenicity (HP; capable of causing significant mortality events in birds). To date, HPAIVs appear o be restricted to the haemagglutinin (HA) glycoprotein H5 and H7 AIV subtypes. Both LPAIV and HPAIV H5 and H7 AIV subtypes are classified as the causative agents of notifiable disease in poultry. A broad range of non-H5/non-H7 LPAIVs also exist that have been associated with more severe disease outcomes in avian species. As a result, the constant threat from AIVs causes significant economic damage in poultry production systems worldwide. The close proximity between mammalian and susceptible avian species in some environments provides the opportunity for both inter-host transmission and mammalian adaptation, potentially resulting in novel AIV strains capable of infecting humans.