Integration of genetic and epidemiological data to infer H5N8 HPAI virus transmission dynamics during the 2016-2017 epidemic in Italy

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.

The application of biosecurity practices for preventing avian influenza in North-Eastern Italy turkey farms: An analysis of the point of view and perception of farmers

INTRODUCTION

Italian and international outbreaks of highly pathogenic avian influenza (HPAI), particularly in densely populated poultry areas (DPPAs), have increased over the past few decades. These emerging risks, which endanger both human and animal health and the entire poultry industry, can be effectively limited by biosecurity measures implemented at human-animal food chain interfaces. Some problems, however, persist in the application of these measures on the part of poultry farmers, prompting the need to explore those aspects and causes that limit their implementation.

MATERIAL AND METHODS

A qualitative approach was selected for the study and a semi-structured interview technique was applied to collect data among turkey farmers (n = 29) working in the north-east of Italy. The aim of this technique was to gather data on farms in order to understand the biosecurity practices adopted and the reasons for and impediments to farmer implementation, or lack thereof. This article presents and discusses the main data collected.

RESULTS

The study revealed that farmers were familiar with the biosecurity measures necessary to contain avian influenza (AI) and other poultry diseases; personal disinfection and animal isolation practices were particularly prominent. Based on the reported procedures, managerial, economic, and psychosocial factors were among the barriers behind the failure to implement biosecurity measures. These obstacles were variously intertwined and associated with the different action settings. In particular management factors, such as lack of time to apply the rules and difficulties contingent on the farm's structural characteristics, mediate the application of biosecurity measures. In terms of communication channels, the company, particularly its technicians, proved to be the primary source of information for farmers in case of emergencies, as well as the primary source of information on the application of biosecurity measures. However, other sources of information were indicated, such as word of mouth among farmers or other non-institutional figures (relatives and acquaintances).

CONCLUSIONS

What emerged, was the need to improve not only the biosecurity management skills, but also to implement forms of cooperation among the various key stakeholders in the poultry sector. The information presented in this pilot study needs to be discussed among competent authorities, public and company veterinarians, company technicians, and farmers. Furthermore, this information will help in participatory co-planning of risk prevention and communication strategies to implement a long-term, sustainable, effective approach to address future epidemic emergencies.

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.

Combined Phylogeographic Analyses and Epidemiologic Contact Tracing to Characterize Atypically Pathogenic Avian Influenza (H3N1) Epidemic, Belgium, 2019

The high economic impact and zoonotic potential of avian influenza call for detailed investigations of dispersal dynamics of epidemics. We integrated phylogeographic and epidemiologic analyses to investigate the dynamics of a low pathogenicity avian influenza (H3N1) epidemic that occurred in Belgium during 2019. Virus genomes from 104 clinical samples originating from 85% of affected farms were sequenced. A spatially explicit phylogeographic analysis confirmed a dominating northeast to southwest dispersal direction and a long-distance dispersal event linked to direct live animal transportation between farms. Spatiotemporal clustering, transport, and social contacts strongly correlated with the phylogeographic pattern of the epidemic. We detected only a limited association between wind direction and direction of viral lineage dispersal. Our results highlight the multifactorial nature of avian influenza epidemics and illustrate the use of genomic analyses of virus dispersal to complement epidemiologic and environmental data, improve knowledge of avian influenza epidemiologic dynamics, and enhance control strategies.

Integration of Epidemiological and Genomic Data to Investigate H5N1 HPAI Outbreaks in Northern Italy in 2021-2022

Between October 2021 and April 2022, 317 outbreaks caused by highly pathogenic avian influenza (HPAI) H5N1 viruses were notified in poultry farms in the northeastern Italian regions. The complete genomes of 214 strains were used to estimate the genetic network based on the similarity of the viruses. An exponential random graph model (ERGM) was used to assess the effect of 'at-risk contacts', 'same owners', 'in-bound/out-bound risk windows overlap', 'genetic differences', 'geographic distances', 'same species', and 'poultry company' on the probability of observing a link within the genetic network, which can be interpreted as the potential propagation of the epidemic via lateral spread or a common source of infection. The variables 'same poultry company' (Est. = 0.548, C.I. = [0.179; 0.918]) and 'risk windows overlap' (Est. = 0.339, C.I. = [0.309; 0.368]) were associated with a higher probability of link formation, while the 'genetic differences' (Est. = -0.563, C.I. = [-0.640; -0.486]) and 'geographic distances' (Est. = -0.058, C.I. = [-0.078; -0.038]) indicated a reduced probability. The integration of epidemiological data with genomic analyses allows us to monitor the epidemic evolution and helps to explain the dynamics of lateral spreads casting light on the potential diffusion routes. The 2021-2022 epidemic stresses the need to further strengthen the biosecurity measures, and to encourage the reorganization of the poultry production sector to minimize the impact of future epidemics.

Connect to Protect: Dynamics and Genetic Connections of Highly Pathogenic Avian Influenza Outbreaks in Poultry from 2016 to 2021 in Germany

During autumn/winter in 2016–2017 and 2020–2021, highly pathogenic avian influenza viruses (HPAIV) caused severe outbreaks in Germany and Europe. Multiple clade 2.3.4.4b H5 HPAI subtypes were responsible for increased mortality in wild birds and high mortality and massive losses in the poultry sector. To clarify putative entry sources and delineate interconnections between outbreaks in poultry holdings and wild birds, we applied whole-genome sequencing and phylodynamic analyses combined with the results of epidemiological outbreak investigations. Varying outbreak dynamics of the distinct reassortants allowed for the identification of individual, putatively wild bird-mediated entries into backyard holdings, several clusters comprising poultry holdings, local virus circulation for several weeks, direct farm-to-farm transmission and potential reassortment within a turkey holding with subsequent spill-over of the novel reassorted virus into the wild bird population. Whole-genome sequencing allowed for a unique high-resolution molecular epidemiology analysis of HPAIV H5Nx outbreaks and is recommended to be used as a standard tool. The presented detailed account of the genetic, temporal, and geographical characteristics of the recent German HPAI H5Nx situation emphasizes the role of poultry holdings as an important source of novel genetic variants and reassortants.

Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe

In winter 2016-7, Europe was severely hit by an unprecedented epidemic of highly pathogenic avian influenza viruses (HPAIVs), causing a significant impact on animal health, wildlife conservation, and livestock economic sustainability. By applying phylodynamic tools to virus sequences collected during the epidemic, we investigated when the first infections occurred, how many infections were unreported, which factors influenced virus spread, and how many spillover events occurred. HPAIV was likely introduced into poultry farms during the autumn, in line with the timing of wild birds' migration. In Germany, Hungary, and Poland, the epidemic was dominated by farm-to-farm transmission, showing that understanding of how farms are connected would greatly help control efforts. In the Czech Republic, the epidemic was dominated by wild bird-to-farm transmission, implying that more sustainable prevention strategies should be developed to reduce HPAIV exposure from wild birds. Inferred transmission parameters will be useful to parameterize predictive models of HPAIV spread. None of the predictors related to live poultry trade, poultry census, and geographic proximity were identified as supportive predictors of HPAIV spread between farms across borders. These results are crucial to better understand HPAIV transmission dynamics at the domestic-wildlife interface with the view to reduce the impact of future epidemics.

Assessing Biosecurity Compliance in Poultry Farms: A Survey in a Densely Populated Poultry Area in North East Italy

Biosecurity in poultry farms represents the first line of defense against the entry and spread of pathogens that may have animal health, food safety, and economic consequences. The aim of this study was to assess biosecurity compliance in poultry farms located in a densely populated poultry area in North East Italy. A total of 259 poultry farms (i.e., broilers, turkeys, and layers) were surveyed between 2018 and 2019 using standardized checklists, and differences in biosecurity compliance between the poultry sectors and years (only for turkey farms) were tested for significance. Among the three sectors, turkey farms showed the highest compliance. Farm hygiene, infrastructure condition, cleaning and disinfection tools, and procedures were the biosecurity measures most complied with. Some deficiencies were observed in the cleanliness of the farm hygiene lock in broiler farms, as well as the presence of the house hygiene lock in broiler and layer farms and an adequate coverage of built-up litter in turkey and broiler farms. In conclusion, this study highlighted a generally high level of biosecurity in the visited poultry farms (probably due to the stringent national regulation and the integration of the poultry industry) and identified some measures that still need to be improved.

Avian influenza overview September - December 2021

Between 16 September and 8 December 2021, 867 highly pathogenic avian influenza (HPAI) virus detections were reported in 27 EU/EEA countries and the UK in poultry (316), in wild (523) and in captive birds (28). The detections in poultry were mainly reported by Italy (167) followed by Hungary and Poland (35 each). Tha majority of the detections in wild birds were reported by Germany (280), Netherlands (65) and United Kingdom (53). The observed persistence and continuous circulation of HPAI viruses in migratory and resident wild birds will continue to pose a risk for the poultry industry in Europe for the coming months. The frequent occurrence of HPAI A(H5) incursions in commercial farms (including poultry production types considered at low avian influenza risk) raises concern about the capacity of the applied biosecurity measures to prevent virus introduction. Short-term preparedness and medium- and long-term prevention strategies, including revising and reinforcing biosecurity measures, reduction of the density of commercial poultry farms and possible appropriate vaccination strategies, should be implemented. The results of the genetic analysis indicate that the viruses characterised during this reporting period belong to clade 2.3.4.4b. Some of the characterized HPAI A(H5N1) viruses detected in Sweden, Germany, Poland and United Kingdom are related to the viruses which have been circulating in Europe since October 2020; in North, Central, South and East Europe novel reassortant A(H5N1) virus has been introduced starting from October 2021. HPAI A(H5N1) was also detected in wild mammal species in Sweden, Estonia and Finland; some of these strains characterised so far present an adaptive marker that is associated with increased virulence and replication in mammals. Since the last report, 13 human infections due to HPAI A(H5N6) and two human cases due to LPAI A(H9N2) virus have been reported from China. Some of these A(H5N6) cases were caused by a reassortant virus of clade 2.3.4.4b, which possessed an HA gene closely related to the A(H5) viruses circulating in Europe. The risk of infection for the general population in the EU/EEA is assessed as low, and for occupationally exposed people, low to medium, with large uncertainty due to the high diversity of circulating viruses in the bird populations.

Elucidating the Local Transmission Dynamics of Highly Pathogenic Avian Influenza H5N6 in the Republic of Korea by Integrating Phylogenetic Information

Highly pathogenic avian influenza (HPAI) virus is one of the most virulent and infectious pathogens of poultry. As a response to HPAI epidemics, veterinary authorities implement preemptive depopulation as a controlling strategy. However, mass culling within a uniform radius of the infection site can result in unnecessary depopulation. Therefore, it is useful to quantify the transmission distance from infected premises (IPs) before determining the optimal area for preemptive depopulation. Accordingly, we analyzed the transmission risk within spatiotemporal clusters of IPs using transmission kernel estimates derived from phylogenetic clustering information on 311 HPAI H5N6 IPs identified during the 2016–2017 epidemic, Republic of Korea. Subsequently, we explored the impact of varying the culling radius on the local transmission of HPAI given the transmission risk estimates. The domestic duck farm density was positively associated with higher transmissibility. Ring culling over a radius of 3 km may be effective for areas with high dense duck holdings, but this approach does not appear to significantly reduce the risk for local transmission in areas with chicken farms. This study provides the first estimation of the local transmission dynamics of HPAI in the Republic of Korea as well as insight into determining an effective ring culling radius.

Spatiotemporal reconstruction and transmission dynamics during the 2016-17 H5N8 highly pathogenic avian influenza epidemic in Italy

Effective control of avian diseases in domestic populations requires understanding of the transmission dynamics facilitating viral emergence and spread. In 2016-17, Italy experienced a significant avian influenza epidemic caused by a highly pathogenic A(H5N8) virus, which affected domestic premises housing around 2.7 million birds, primarily in the north-eastern regions with the highest density of poultry farms (Lombardy, Emilia-Romagna and Veneto). We perform integrated analyses of genetic, spatiotemporal and host data within a Bayesian phylogenetic framework. Using continuous and discrete phylogeography, we estimate the locations of movements responsible for the spread and persistence of the epidemic. The information derived from these analyses on rates of transmission between regions through time can be used to assess the success of control measures. Using an approach based on phylogenetic-temporal distances between domestic cases, we infer the presence of cryptic wild bird-mediated transmission, information that can be used to complement existing epidemiological methods for distinguishing transmission within the domestic population from incursions across the wildlife-domestic interface, a common challenge in veterinary epidemiology. Spatiotemporal reconstruction of the epidemic reveals a highly skewed distribution of virus movements with a high proportion of shorter distance local movements interspersed with occasional long-distance dispersal events associated with wild birds. We also show how such inference be used to identify possible instances of human-mediated movements where distances between phylogenetically linked domestic cases are unusually high.

Different environmental gradients associated to the spatiotemporal and genetic pattern of the H5N8 highly pathogenic avian influenza outbreaks in poultry in Italy

Comprehensive understanding of the patterns and drivers of avian influenza outbreaks is pivotal to inform surveillance systems and heighten nations' ability to quickly detect and respond to the emergence of novel viruses. Starting in early 2017, the Italian poultry sector has been involved in the massive H5N8 highly pathogenic avian influenza epidemic that spread in the majority of the European countries in 2016/2017. Eighty-three outbreaks were recorded in north-eastern Italy, where a densely populated poultry area stretches along the Lombardy, Emilia-Romagna and Veneto regions. The confirmed cases, affecting both the rural and industrial sectors, depicted two distinct epidemic waves. We adopted a combination of multivariate statistics techniques and multi-model regression selection and inference, to investigate how environmental factors relate to the pattern of outbreaks diversity with respect to their spatiotemporal and genetic diversity. Results showed that a combination of eco-climatic and host density predictors were associated with the outbreaks pattern, and variation along gradients was noticeable among genetically and geographically distinct groups of avian influenza cases. These regional contrasts may be indicative of a different mechanism driving the introduction and spreading routes of the influenza virus in the domestic poultry population. This methodological approach may be extended to different spatiotemporal scale to foster site-specific, ecologically informed risk mitigating strategies.

Genetic incompatibilities and reduced transmission in chickens may limit the evolution of reassortants between H9N2 and panzootic H5N8 clade 2.3.4.4 avian influenza virus showing high virulence for mammals

The unprecedented spread of H5N8- and H9N2-subtype avian influenza virus (AIV) in birds across Asia, Europe, Africa, and North America poses a serious public health threat with a permanent risk of reassortment and the possible emergence of novel virus variants with high virulence in mammals. To gain information on this risk, we studied the potential for reassortment between two contemporary H9N2 and H5N8 viruses. While the replacement of the PB2, PA, and NS genes of highly pathogenic H5N8 by homologous segments from H9N2 produced infectious H5N8 progeny, PB1 and NP of H9N2 were not able to replace the respective segments from H5N8 due to residues outside the packaging region. Furthermore, exchange of the PB2, PA, and NS segments of H5N8 by those of H9N2 increased replication, polymerase activity and interferon antagonism of the H5N8 reassortants in human cells. Notably, H5N8 reassortants carrying the H9N2-subtype PB2 segment and to lesser extent the PA or NS segments showed remarkably increased virulence in mice as indicated by rapid onset of mortality, reduced mean time to death and increased body weight loss. Simultaneously, we observed that in chickens the H5N8 reassortants, particularly with the H9N2 NS segment, demonstrated significantly reduced transmission to co-housed chickens. Together, while the limited capacity for reassortment between co-circulating H9N2 and H5N8 viruses and the reduced bird-to-bird transmission of possible H5N8 reassortants in chickens may limit the evolution of such reassortant viruses, they show a higher replication potential in human cells and increased virulence in mammals.

Genesis and spread of multiple reassortants during the 2016/2017 H5 avian influenza epidemic in Eurasia

In 2016/2017, highly pathogenic avian influenza (HPAI) virus of the subtype H5 spilled over into wild birds and caused the largest known HPAI epidemic in Europe, affecting poultry and wild birds. During its spread, the virus frequently exchanged genetic material (reassortment) with cocirculating low-pathogenic avian influenza viruses. To determine where and when these reassortments occurred, we analyzed Eurasian avian influenza viruses and identified a large set of H5 HPAI reassortants. We found that new genetic material likely came from wild birds across their migratory range and from domestic ducks not only in China, but also in central Europe. This knowledge is important to understand how the virus could adapt to wild birds and become established in wild bird populations.

Highly pathogenic avian influenza (HPAI) viruses of the H5 A/goose/Guangdong/1/96 lineage can cause severe disease in poultry and wild birds, and occasionally in humans. In recent years, H5 HPAI viruses of this lineage infecting poultry in Asia have spilled over into wild birds and spread via bird migration to countries in Europe, Africa, and North America. In 2016/2017, this spillover resulted in the largest HPAI epidemic on record in Europe and was associated with an unusually high frequency of reassortments between H5 HPAI viruses and cocirculating low-pathogenic avian influenza viruses. Here, we show that the seven main H5 reassortant viruses had various combinations of gene segments 1, 2, 3, 5, and 6. Using detailed time-resolved phylogenetic analysis, most of these gene segments likely originated from wild birds and at dates and locations that corresponded to their hosts’ migratory cycles. However, some gene segments in two reassortant viruses likely originated from domestic anseriforms, either in spring 2016 in east China or in autumn 2016 in central Europe. Our results demonstrate that, in addition to domestic anseriforms in Asia, both migratory wild birds and domestic anseriforms in Europe are relevant sources of gene segments for recent reassortant H5 HPAI viruses. The ease with which these H5 HPAI viruses reassort, in combination with repeated spillovers of H5 HPAI viruses into wild birds, increases the risk of emergence of a reassortant virus that persists in wild bird populations yet remains highly pathogenic for poultry.

Pathogenicity of clade 2.3.2.1 H5N1 highly pathogenic avian influenza virus in American kestrel (Falco sparverius)

Birds of prey, including endangered species, have been infected with H5 highly pathogenic avian influenza viruses (HPAIVs) in several countries. In this present study, we assessed the pathogenicity of the clade 2.3.2.1 H5N1 HPAIV in American kestrels (Falco sparverius) with a view to preventing future outbreaks in raptors. The kestrels were intranasally inoculated with the virus or fed the meat of chicks that had died from viral infection. Kestrels in both groups initially had reduced food intake, showed clinical signs such as depression and neurologic manifestations, and succumbed to the infection within 6 days. The kestrels primarily shed the virus orally from 1 day post-inoculation until death, with an average titre of 10^4.5-5.7 EID₅₀/ml, which is comparable to the inoculum titre. The viruses replicated in almost all tested tissues; notably, the feather calamuses also contained infectious virions and/or viral genes. Pancreatic lesions were present in several infected birds, as shown in previous cases of HPAIV infection in raptors. These results indicate that kestrels are highly susceptible to infection by clade 2.3.2.1 H5 HPAIVs, which readily occurs through the consumption of infected bird carcasses. Early detection and removal of HPAIV infected carcasses in the field is essential for preventing outbreaks in raptors. RESEARCH HIGHLIGHTS Clade 2.3.2.1 H5 HPAIV caused lethal infection in American kestrels. Kestrels with the HPAIV showed neurologic signs and eye disorders. The HPAIV replicated in systemic tissues of kestrels, and was orally shed. The HPAIV was recovered from feather calamus of kestrels.

Association of wild bird densities around poultry farms with the risk of highly pathogenic avian influenza virus subtype H5N8 outbreaks in the Netherlands, 2016

Highly pathogenic (HP) avian influenza viruses (AIV) can spread globally through migratory birds and cause massive outbreaks in commercial poultry. AIV outbreaks have been associated with proximity to waterbodies, presence of waterfowl or wild bird cases near poultry farms. In this study, we compared densities of selected HPAI high‐risk wild bird species around 7 locations (H farms) infected with HPAIV H5N8 in the Netherlands in 2016–2017 to densities around 21 non‐infected reference farms. Nine reference farms were in low‐lying water‐rich areas (R‐W) and 12 in higher non‐water‐rich areas (R‐NW). Average monthly numbers/km² of Eurasian wigeons, tufted ducks, Anatidae (ducks, geese and swans) and Laridae (gulls) were calculated between September and April in rings of 0–1, 1–3, 3–6 and 6–10 km around the farms. Linear mixed model analyses showed generally higher bird densities for H and R‐W compared to R‐NW farms between October and March. This was most striking for Eurasian wigeons, with in peak month December 105 (95% CI:17–642) and 40 (7–214) times higher densities around H and R‐W farms, respectively, compared to R‐NW farms. Increased densities around H farms for Eurasian wigeons and Anatidae were more pronounced for distances up to 10 km compared to 0–1 km that mostly consists of the farm yard, which is an unattractive habitat for waterfowl. This distance effect was not observed in gulls, nor in tufted ducks that live on large open waterbodies which are unlikely to be within 0–1 km of farms. This study provides insights into spatio‐temporal density dynamics of HPAI high‐risk birds around farms and their associations with poultry outbreaks. The outcomes indicate that knowledge of environmental and ecological drivers for wild bird presence and abundance may facilitate identification of priority areas for surveillance and biosecurity measures and decisions on establishments of poultry farms to reduce risk of HPAI outbreaks.

Pandemic potential of highly pathogenic avian influenza clade 2.3.4.4 A(H5) viruses

The panzootic caused by A/goose/Guangdong/1/96‐lineage highly pathogenic avian influenza (HPAI) A(H5) viruses has occurred in multiple waves since 1996. From 2013 onwards, clade 2.3.4.4 viruses of subtypes A(H5N2), A(H5N6), and A(H5N8) emerged to cause panzootic waves of unprecedented magnitude among avian species accompanied by severe losses to the poultry industry around the world. Clade 2.3.4.4 A(H5) viruses have expanded in distinct geographical and evolutionary pathways likely via long distance migratory bird dispersal onto several continents and by poultry trade among neighboring countries. Coupled with regional circulation, the viruses have evolved further by reassorting with local viruses. As of February 2019, there have been 23 cases of humans infected with clade 2.3.4.4 H5N6 viruses, 16 (70%) of which had fatal outcomes. To date, no HPAI A(H5) virus has caused sustainable human‐to‐human transmission. However, due to the lack of population immunity in humans and ongoing evolution of the virus, there is a continuing risk that clade 2.3.4.4 A(H5) viruses could cause an influenza pandemic if the ability to transmit efficiently among humans was gained. Therefore, multisectoral collaborations among the animal, environmental, and public health sectors are essential to conduct risk assessments and develop countermeasures to prevent disease and to control spread. In this article, we describe an assessment of the likelihood of clade 2.3.4.4 A(H5) viruses gaining human‐to‐human transmissibility and impact on human health should such human‐to‐human transmission occur. This structured analysis assessed properties of the virus, attributes of the human population, and ecology and epidemiology of these viruses in animal hosts.

Structural and antigenic characterization of a computationally-optimized H5 hemagglutinin influenza vaccine

Influenza A virus is a leading cause of death worldwide. Viruses of the H5 subtype have the potential to induce high mortality, and no vaccines are currently available to protect against H5 influenza viruses in the event of an outbreak. Experimental vaccination with one clade 2 virus does not protect against other subclades. The computationally optimized broadly reactive (COBRA) methodology was previously used to generate a H5 hemagglutinin (HA) antigen (COBRA2) that elicited increased serological breadth against multiple clade 2 H5N1 influenza viruses. In this report, we structurally and antigenically characterized the COBRA2 HA antigen. We examined the biochemical characteristics of the COBRA2 protein and determined the protein is correctly cleaved, properly folded into a trimeric structure, and antigenically correct by probing with HA head- and stem-specific monoclonal antibodies (mAbs). We further probed the antigenicity by examining binding of a panel of H5 mouse mAbs to the COBRA2 antigen, as well as several other HA antigens. We determined the X-ray crystal structure of the COBRA2 HA antigen to 2.8 Å and the protein was observed to be in the expected trimeric form. The COBRA2 HA was structurally similar to the naturally occurring H5 HA antigens and suggests the protein folds similar to known HA structures. Overall, our data allow us to formulate a hypothesis on the mechanism of increased breadth due to vaccination with the COBRA2 HA antigen, which is that the protein incorporates antigenic sites from numerous HA antigens, and elicits mAbs with limited breadth, but with diversity in targeted antigenic sites.