Molecular epidemiology of infectious bursal disease virus in the Near East and Persian Gulf regions.

RESEARCH HIGHLIGHTS: Different field IBDVs were found to circulate in the Near and Middle East.Multiple atypical genotypes (A3B1, A4B1, A6B1) were found to circulate extensively.Traditional very virulent IBDVs (A3B2) were a minority of the detected strains.Viral exchanges can be hypothesized between the region and different continents.

Infectious bursal disease virus in Western Europe: the rise of reassortant strains as the dominant field threat.

Infectious bursal disease virus (IBDV) is a highly contagious birnavirus causing a burdensome immunosuppressive disease in chickens. IBDV features a remarkable antigenic, pathogenic and genetic heterogeneity, with significant implications on disease manifestation, control measures and diagnostic approaches. The recent proposals of comprehensive phylogenetic classification systems offered the ideal platform for large-scale molecular surveys, which are crucial to gather epidemiological data and inform control efforts. In this study, the IBDV scenario was investigated in most of Western Europe by considering the results of diagnostic activities performed internationally throughout 2021. In total, 470 bursal samples from nine different countries were analysed by RT-PCR targeting the VP2. When a field virus was identified, the VP1 was also characterized. Most of the 132 detected field viruses were highly homologous reassortants featuring a very virulent-like VP2 and a classical-like VP1 (genotype A3B1). Despite emerging recently, these reassortants were already signalled in several countries in North-Western Europe and associated with subclinical infections. Here, we report their further spread in the region, where they currently represent the dominant field threat. Two other IBDV types were found, one in Italy, where all the identified viruses clustered in a clade of the A3B1 genotype previously reported only in Russia and the Middle East, and the other in Portugal, where the recently characterized A9B1 genotype was confirmed to circulate. The obtained data suggest the recent occurrence of a major shift in the Western European epidemiological landscape of IBDV, stressing the importance of steady monitoring and sharing of information among different countries and laboratories.RESEARCH HIGHLIGHTS The IBDV scenario in Western Europe seems to have radically changed in recent years.IBDV reassortants were found to be the dominant field type in the region.Local circulation of two other IBDV types was detected in Italy and Portugal.

First detection of avian metapneumovirus subtype C Eurasian lineage in a Eurasian wigeon (Mareca penelope) wintering in Northeastern Italy: an additional hint on the role of migrating birds in the viral epidemiology.

Avian metapneumovirus (aMPV) economically affects the global poultry industry causing respiratory and reproductive disorders. Considering the paucity of data on aMPV occurrence in European free-ranging avifauna, a molecular survey was conducted on wild birds of 23 species belonging to the orders Anseriformes, Charadriiformes or Passeriformes, captured alive and sampled in Northeast Italy as part of the national avian influenza virus (AIV) surveillance activities. A total of 492 oropharyngeal swabs, collected from 2007-2010, all AIV-negative, were screened from aMPV by subtype-specific qRT-PCR. An aMPV-C strain, named aMPV/C/IT/Wigeon/758/07, was found in a wintering young Eurasian wigeon (Mareca penelope) sampled in November 2007. The matrix, fusion, and attachment glycoprotein genes of the detected strain were subsequently amplified by specific independent RT-PCRs, then sequenced, and compared in a phylogenetic framework with known aMPV homologous sequences retrieved from GenBank. Close genetic relationships were found between the aMPV/C/IT/Wigeon/758/07 strain and subtype C Eurasian lineage strains isolated in the late 1990s in French domestic ducks, suggesting epidemiological links. Eurasian wigeons are medium/long-range migrant dabbling ducks that move along the Black Sea/Mediterranean flyway; our finding might, therefore, be related to migratory bridges between countries. To our knowledge, this is the first molecular evidence of the occurrence of aMPV subtype C in Italy and backdates the aMPV-C circulation to 2007. Moreover, the results suggest the susceptibility of Eurasian wigeons to aMPV. Broader investigations are needed to assess the role of wild ducks and the significance of the wildfowl/poultry interface in aMPV-C epidemiology.RESEARCH HIGHLIGHTSWild birds live-captured in Italy were tested for aMPV detection and characterization.aMPV-C Eurasian lineage was found for the first time in a wintering Eurasian wigeon.Migratory birds could be involved in the aMPV epidemiology.

Detection and molecular characterization of a new genotype of infectious bursal disease virus in Portugal.

RESEARCH HIGHLIGHTSEight IBDV strains with unique VP2 features were detected in Portugal.Based on two distinct classification methods, the strains belong to a new genotype.

Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues.

BACKGROUND: Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. RESULTS: The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. CONCLUSIONS: The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.

Effect of assay choice, viral concentration and operator interpretation on infectious bronchitis virus detection and characterization.

Despite the efforts to achieve a consistent classification scheme based on the complete S1 gene, the genetic characterization of infectious bronchitis virus (IBV) is often performed on partial S1 regions due to economic and time constraints in the diagnostic routine. Sanger sequencing remains the most common and cost-effective option even if the analysis of samples where multiple field and vaccine strain populations coexist can lead to partial or misleading results. The present study aimed to evaluate the different diagnostic outcomes of three commonly used RT-PCR methods targeting two regions of the S1 gene. A possible bias in IBV detection and characterization was investigated in relation to the adopted method, the strain concentration as well as their ratio in mixed samples. Thirty samples were prepared by artificially mixing two vaccine strains, combined at different ratios and selected among four different IBV lineages, i.e. GI-1 (Mass), GI-13 (793/B), GI-19 (QX), GI-23 (Israeli Variant 2). Sequence analysis was conducted both manually and with bioinformatic methods. The result agreement among methods, replicates and analysis approaches was statistically evaluated. Consistent results emerged among the three assays, with a few discrepancies likely caused by primer affinity and target amount. This study confirms the complexity of IBV strain identification and highlights the importance of evaluating and updating the available diagnostic assays for a reliable detection of all circulating IBV strains.

Avian Metapneumovirus subtype B around Europe: a phylodynamic reconstruction.

Avian Metapneumovirus (aMPV) has been recognized as a respiratory pathogen of turkey and chickens for a long time. Recently, a crescent awareness of aMPV, especially subtype B, clinical and economic impact has risen among European researchers and veterinarians. Nevertheless, the knowledge of its epidemiology and evolution is still limited. In the present study, the broadest available collection of partial G gene sequences obtained from European aMPV-B strains was analyzed using different phylodynamic and biostatistical approaches to reconstruct the viral spreading over time and the role of different hosts on its evolution. After aMPV-B introduction, approximatively in 1985 in France, the infection spread was relatively quick, involving the Western and Mediterranean Europe until the end of the 1990s, and then spreading westwards at the beginning of the new millennium, in parallel with an increase of viral population size. In the following period, a wider mixing among aMPV-B strains detected in eastern and western countries could be observed. Most of the within-country genetic heterogeneity was ascribable to single or few introduction events, followed by local circulation. This, combined with the high evolutionary rate herein demonstrated, led to the establishment of genetically and phenotypically different clusters among countries, which could affect the efficacy of natural or vaccine-induced immunity and should be accounted for when planning control measure implementation. On the contrary, while a significant strain exchange was proven among turkey, guinea fowl and chicken, no evidence of differential selective pressures or specific amino-acid mutations was observed, suggesting that no host adaptation is occurring.

Evolution of infectious bronchitis virus in the field after homologous vaccination introduction.

Despite the fact that vaccine resistance has been typically considered a rare phenomenon, some episodes of vaccine failure have been reported with increasing frequency in intensively-raised livestock. Infectious bronchitis virus (IBV) is a widespread avian coronavirus, whose control relies mainly on extensive vaccine administration. Unfortunately, the continuous emergence of new vaccine-immunity escaping variants prompts the development of new vaccines. In the present work, a molecular epidemiology study was performed to evaluate the potential role of homologous vaccination in driving IBV evolution. This was undertaken by assessing IBV viral RNA sequences from the ORF encoding the S1 portion of viral surface glycoprotein (S) before and after the introduction of a new live vaccine on broiler farms in northern-Italy. The results of several biostatistics analyses consistently demonstrate the presence of a higher pressure in the post-vaccination period. Natural selection was detected essentially on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. This evidence strongly supports the action of vaccine-induced immunity in conditioning viral evolution, potentially leading to the emergence of new vaccine-escape variants. The great plasticity of rapidly-evolving RNA-viruses in response to human intervention, which extends beyond the poultry industry, is demonstrated, claiming further attention due to their relevance for animal and especially human health.

Tracing the Flight: Investigating the Introduction of Avian Metapneumovirus (aMPV) A and B.

Avian metapneumovirus (aMPV) has been identified as an important cause of respiratory and reproductive disease, leading to significant productive losses worldwide. Different subtypes have been found to circulate in different regions, with aMPV-A and B posing a significant burden especially in the Old World, and aMPV-C in North America, albeit with limited exceptions of marginal economic relevance. Recently, both aMPV-A and aMPV-B have been reported in the U.S.; however, the route of introduction has not been investigated. In the present study, the potential importation pathways have been studied through phylogenetic and phylodynamic analyses based on a broad collection of partial attachment (G) protein sequences collected worldwide. aMPV-B circulating in the U.S. seems the descendant of Eastern Asian strains, which, in turn, are related to European ones. A likely introduction pathway mediated by wild bird migration through the Beringian crucible, where the East Asian and Pacific American flight paths intersect, appears likely and was previously reported for avian influenza. aMPV-A, on the other hand, showed a Mexican origin, involving strains related to Asian ones. Given the low likelihood of trade or illegal importation, the role of wild birds appears probable also in this case, since the region is covered by different flight paths directed in a North-South direction through America. Since the information on the role of wild birds in aMPV epidemiology is still scarce and scattered, considering the significant practical implications for the poultry industry demonstrated by recent U.S. outbreaks, further surveys on wild birds are encouraged.

The Effect of Global Spread, Epidemiology, and Control Strategies on the Evolution of the GI-19 Lineage of Infectious Bronchitis Virus.

The GI-19 lineage of infectious bronchitis virus (IBV) has emerged as one of the most impactful, particularly in the "Old World". Originating in China several decades ago, it has consistently spread and evolved, often forming independent clades in various areas and countries, each with distinct production systems and control strategies. This study leverages this scenario to explore how different environments may influence virus evolution. Through the analysis of the complete S1 sequence, four datasets were identified, comprising strains of monophyletic clades circulating in different continents or countries (e.g., Asia vs. Europe and China vs. Thailand), indicative of single introduction events and independent evolution. The population dynamics and evolutionary rate variation over time, as well as the presence and intensity of selective pressures, were estimated and compared across these datasets. Since the lineage origin (approximately in the mid-20th century), a more persistent and stable viral population was estimated in Asia and China, while in Europe and Thailand, a sharp increase following the introduction (i.e., 2005 and 2007, respectively) of GI-19 was observed, succeeded by a rapid decline. Although a greater number of sites on the S1 subunit were under diversifying selection in the Asian and Chinese datasets, more focused and stronger pressures were evident in both the European (positions 2, 52, 54, 222, and 379 and Thai (i.e., positions 10, 12, 32, 56, 62, 64, 65, 78, 95, 96, 119, 128, 140, 182, 292, 304, 320, and 323) strains, likely reflecting a more intense and uniform application of vaccines in these regions. This evidence, along with the analysis of control strategies implemented in different areas, suggests a strong link between effective, systematic vaccine implementation and infection control. However, while the overall evolutionary rate was estimated at approximately 10-3 to 10-4, a significant inverse correlation was found between viral population size and the rate of viral evolution over time. Therefore, despite the stronger selective pressure imposed by vaccination, effectively constraining the former through adequate control strategies can efficiently prevent viral evolution and the emergence of vaccine-escaping variants.

Reconstruction of Avian Reovirus History and Dispersal Patterns: A Phylodynamic Study.

Avian reovirus (ARV) infection can cause significant losses to the poultry industry. Disease control has traditionally been attempted mainly through vaccination. However, the increase in clinical outbreaks in the last decades demonstrated the poor effectiveness of current vaccination approaches. The present study reconstructs the evolution and molecular epidemiology of different ARV genotypes using a phylodynamic approach, benefiting from a collection of more than one thousand sigma C (σC) sequences sampled over time at a worldwide level. ARVs' origin was estimated to occur several centuries ago, largely predating the first clinical reports. The origins of all genotypes were inferred at least one century ago, and their emergence and rise reflect the intensification of the poultry industry. The introduction of vaccinations had only limited and transitory effects on viral circulation and further expansion was observed, particularly after the 1990s, likely because of the limited immunity and the suboptimal and patchy vaccination application. In parallel, strong selective pressures acted with different strengths and directionalities among genotypes, leading to the emergence of new variants. While preventing the spread of new variants with different phenotypic features would be pivotal, a phylogeographic analysis revealed an intricate network of viral migrations occurring even over long distances and reflecting well-established socio-economic relationships.

Exploring Variability: Inflammation Mediator Levels across Tissues and Time in Poultry Experimentally Infected by the G1a and G6 Genogroups of Infectious Bursal Disease Virus (IBDV).

Infectious bursal disease virus (IBDV) is a significant burden for poultry production and market due to both direct disease and induced immunosuppression. In the present study, the expression of different cytokines in the bursa of Fabricius and thymus was evaluated during a 28-day-long experimental infection with two strains classified in the G1a (Classical) and G6 (ITA) genogroups. Although both strains significantly affected and modulated the expression of different molecules, the G6 strain seemed to induce a delayed immune response or suppress it more promptly. A recovery in the expression of several mediators was observed in the G1a-infected group at the end of the study, but not in the G6 one, further supporting a more persistent immunosuppression. This evidence fits with the higher replication level previously reported for the G6 and with the clinical outcome, as this genotype, although subclinical, has often been considered more immunosuppressive. However, unlike other studies focused on shorter time periods after infection, the patterns observed in this paper were highly variable and complex, depending on the strain, tissue, and time point, and characterized by a non-negligible within-group variability. Besides confirming the strain/genogroup effect on immune system modulation, the present study suggests the usefulness of longer monitoring activities after experimental infection to better understand the complex patterns and interactions with the host response.

D for dominant: porcine circovirus 2d (PCV-2d) prevalence over other genotypes in wild boars and higher viral flows from domestic pigs in Italy.

Introduction: Porcine circovirus 2 (PCV-2) is a key pathogen for the swine industry at a global level. Nine genotypes, differing in epidemiology and potentially virulence, emerged over time, with PCV-2a, -2b, and -2d being the most widespread and clinically relevant. Conversely, the distribution of minor genotypes appears geographically and temporally restricted, suggesting lower virulence and different epidemiological drivers. In 2022, PCV-2e, the most genetically and phenotypically divergent genotype, was identified in multiple rural farms in North-eastern Italy. Since rural pigs often have access to outdoor environment, the introduction from wild boars was investigated. Methods: Through a molecular and spatial approach, this study investigated the epidemiology and genetic diversity of PCV-2 in 122 wild boars across different provinces of North-eastern Italy. Results: Molecular analysis revealed a high PCV-2 frequency (81.1%, 99/122), and classified the majority of strains as PCV-2d (96.3%, 78/81), with sporadic occurrences of PCV-2a (1.2%, 1/81) and PCV-2b (2.5%, 2/81) genotypes. A viral flow directed primarily from domestic pigs to wild boars was estimated by phylogenetic and phylodynamic analyses. Discussion: These findings attested that the genotype replacement so far described only in the Italian domestic swine sector occurred also in wild boars. and suggested that the current heterogeneity of PCV-2d strains in Italian wild boars likely depends more on different introduction events from the domestic population rather than the presence of independent evolutionary pressures. While this might suggest PCV-2 circulation in wild boars having a marginal impact in the industrial sector, the sharing of PCV-2d strains across distinct wild populations, in absence of a consistent geographical pattern, suggests a complex interplay between domestic and wild pig populations, emphasizing the importance of improved biosecurity measures to mitigate the risk of pathogen transmission.

When Everything Becomes Bigger: Big Data for Big Poultry Production.

In future decades, the demand for poultry meat and eggs is predicted to considerably increase in pace with human population growth. Although this expansion clearly represents a remarkable opportunity for the sector, it conceals a multitude of challenges. Pollution and land erosion, competition for limited resources between animal and human nutrition, animal welfare concerns, limitations on the use of growth promoters and antimicrobial agents, and increasing risks and effects of animal infectious diseases and zoonoses are several topics that have received attention from authorities and the public. The increase in poultry production must be achieved mainly through optimization and increased efficiency. The increasing ability to generate large amounts of data ("big data") is pervasive in both modern society and the farming industry. Information accessibility-coupled with the availability of tools and computational power to store, share, integrate, and analyze data with automatic and flexible algorithms-offers an unprecedented opportunity to develop tools to maximize farm profitability, reduce socio-environmental impacts, and increase animal and human health and welfare. A detailed description of all topics and applications of big data analysis in poultry farming would be infeasible. Therefore, the present work briefly reviews the application of sensor technologies, such as optical, acoustic, and wearable sensors, as well as infrared thermal imaging and optical flow, to poultry farming. The principles and benefits of advanced statistical techniques, such as machine learning and deep learning, and their use in developing effective and reliable classification and prediction models to benefit the farming system, are also discussed. Finally, recent progress in pathogen genome sequencing and analysis is discussed, highlighting practical applications in epidemiological tracking, and reconstruction of microorganisms' population dynamics, evolution, and spread. The benefits of the objective evaluation of the effectiveness of applied control strategies are also considered. Although human-artificial intelligence collaborations in the livestock sector can be frightening because they require farmers and employees in the sector to adapt to new roles, challenges, and competencies-and because several unknowns, limitations, and open-ended questions are inevitable-their overall benefits appear to be far greater than their drawbacks. As more farms and companies connect to technology, artificial intelligence (AI) and sensing technologies will begin to play a greater role in identifying patterns and solutions to pressing problems in modern animal farming, thus providing remarkable production-based and commercial advantages. Moreover, the combination of diverse sources and types of data will also become fundamental for the development of predictive models able to anticipate, rather than merely detect, disease occurrence. The increasing availability of sensors, infrastructures, and tools for big data collection, storage, sharing, and analysis-together with the use of open standards and integration with pathogen molecular epidemiology-have the potential to address the major challenge of producing higher-quality, more healthful food on a larger scale in a more sustainable manner, thereby protecting ecosystems, preserving natural resources, and improving animal and human welfare and health.

Vaccine Interaction and Protection against Virulent Avian Metapneumovirus (aMPV) Challenge after Combined Administration of Newcastle Disease and aMPV Live Vaccines to Day-Old Turkeys.

Newcastle disease virus (NDV) and avian metapneumovirus (aMPV) are among the most impactful pathogens affecting the turkey industry. Since turkeys are routinely immunized against both diseases, the hatchery administration of the combined respective live vaccines would offer remarkable practical advantages. However, the compatibility of NDV and aMPV vaccines has not yet been experimentally demonstrated in this species. To address this issue, an aMPV subtype B live vaccine was administered to day-old poults either alone or in combination with one of two different ND vaccines. The birds were then challenged with a virulent aMPV subtype B strain, clinical signs were recorded and aMPV and NDV vaccine replication and humoral immune response were assessed. All results supported the absence of any interference hampering protection against aMPV, with no significant differences in terms of clinical scoring. In addition, the mean aMPV vaccine viral titers and antibody titers measured in the dual vaccinated groups were comparable or even higher than in the group vaccinated solely against aMPV. Lastly, based on the NDV viral and antibody titers, the combined aMPV and NDV vaccination does not seem to interfere with protection against NDV, although further studies involving an actual ND challenge will be necessary to fully demonstrate this hypothesis.

Conflicting Evidence between Clinical Perception and Molecular Epidemiology: The Case of Fowl Adenovirus D.

Fowl adenoviruses (FAdVs, species FAdV-A/-E) are responsible for several clinical syndromes reported with increasing frequency in poultry farms in the last decades. In the present study, a phylodynamic analysis was performed on a group of FAdV-D Hexon sequences with adequate available metadata. The obtained results demonstrated the long-term circulation of this species, at least several decades before the first identification of the disease. After a period of progressive increase, the viral population showed a high-level circulation from approximately the 1960s to the beginning of the new millennium, mirroring the expansion of intensive poultry production and animal trade. At the same time, strain migration occurred mainly from Europe to other continents, although other among-continent connections were estimated. Thereafter, the viral population declined progressively, likely due to the improved control measures, potentially including the development and application of FAdV vaccines. An increase in the viral evolutionary rate featured this phase. A role of vaccine-induced immunity in shaping viral evolution could thus be hypothesized. Accordingly, several sites of the Hexon, especially those targeted by the host response were proven under a significant pervasive or episodic diversifying selection. The present study results demonstrate the role of intensive poultry production and market globalization in the rise of FAdV. The applied control strategies, on the other hand, were effective in limiting viral circulation and shaping its evolution.

Comparison between Sampling Techniques for Virological Molecular Analyses: Dolphin Morbillivirus and Herpesvirus Detection from FTA® Card and Frozen Tissue.

Stranded animals offer valuable information on marine mammal physiology and pathology; however, the decomposition state of the carcasses and lack of a rigorous cold chain for sample preservation can sometimes discourage diagnostic analyses based on nucleic acid detection. The present paper aims at evaluating the reliability of FTA® card tissue imprints as an alternative matrix to frozen tissues for virological analyses based on biomolecular methods. Given the contribution of Cetacean morbillivirus (CeMV) to strandings and the increase of herpesvirus detection in cetaceans, these two pathogens were selected as representative of RNA and DNA viruses. Dolphin morbillivirus (DMV) and herpesvirus presence was investigated in parallel on tissue imprints on FTA® cards and frozen tissues collected during necropsy of dolphins stranded in Italy. Samples were analysed by nested RT-PCR for DMV and nested-PCR for herpesvirus. Only one animal was positive for herpesvirus, hampering further considerations on this virus. DMV was detected in all animals, both in FTA® card imprints and tissue samples, with differences possibly related to the decomposition condition category of the carcasses. Tissue sampling on FTA® cards seems a promising alternative to frozen tissues for biomolecular analyses, especially when ensuring adequate storage and shipment conditions for frozen tissues is difficult.

Peste Des Petits Ruminants in the Middle East: Epidemiological Situation and Status of Control and Eradication Activities after the First Phase of the PPR Global Eradication Program (2017-2021).

Peste des petits ruminants (PPR) is a burdensome viral disease primarily affecting small ruminants, which is currently targeted for eradication by 2030 through the implementation of a Global Control and Eradication Strategy (PPR GCES). The PPR GCES, launched in 2015, has strongly encouraged countries to participate in Regional PPR Roadmaps, designated according to the Food and Agricultural Organization of the United Nations (FAO) and World Organisation for Animal Health (WOAH) regions and epidemiological considerations, with each targeted by dedicated meetings and activities. Following the conclusion of the first phase of the PPR Global Eradication Program (PPR GEP) (2017-2021), the present work focuses on the disease situation and status of the eradication campaign in the fourteen countries of the PPR GCES Middle Eastern Roadmap as well as Egypt. PPR is endemic to or suspected to be present in most of the region, except for Bahrain, which, as of 2021, is preparing to apply for official recognition as being free of PPR. Some substantial shortcomings are observed in surveillance and disease reporting, as well as in the implemented control strategies, most notably vaccination. Since many of these limitations are shared by many of the investigated countries, the international cooperation and harmonization of control efforts appears crucial to making PPR eradication attainable in the Middle East.

Into the backyard: Multiple detections of PCV-2e in rural pig farms of Northern Italy. An unexpected ecological niche?

Porcine circovirus type 2 (PCV-2) is among the most burdensome viruses of the swine industry globally. Several genotypes have been periodically emerging, but just three of them (PCV-2a, PCV-2b, and PCV-2d) seem to circulate worldwide and be associated with the disease. Conversely, the spatial-temporal distribution of minor genotypes appears limited and their clinical relevance is still unclear. Recently PCV-2e was incidentally detected for the first time in Europe in a breeding farm in Northeastern Italy, while no connection could be established with countries where this genotype had been previously detected. To investigate circulating genotypes in the neglected rural context and provide a comparison with the most explored industrial context, a molecular survey was performed on samples collected in rural (n = 72) and industrial farms (n = 110) located in the same geographic area. Phylogenetic analysis surprisingly evidenced PCV-2e circulation only in pigs reared in backyard farms (n = 5), while major genotypes (PCV-2a, -2b, -2d) circulate in both rearing contexts. However, the close genetic similarity between the herein detected PCV-2e strains and the previously reported one testify that, although unusual, such rural-to-industrial strains exchange affected also PCV-2e. The greater genetic and phenotypic diversity of PCV-2e genotype compared to other ones might threaten the protection granted by current vaccines. The present study suggests the rural context as an ecological niche for the circulation of PCV-2e, and even of other minor genotypes. PCV-2e detection in pigs with outdoor access further stresses the epidemiological role of backyard farms as interfaces for pathogen introduction, potentially ascribable to the different rearing approaches, lower managerial and biosecurity capabilities, and easier contacts with wildlife.

First Detection and Molecular Characterization of Novel Variant Infectious Bursal Disease Virus (Genotype A2dB1b) in Egypt.

Infectious bursal disease (IBD) is an immunosuppressive disease causing significant damage to the poultry industry worldwide. Its etiological agent is infectious bursal disease virus (IBDV), a highly resistant RNA virus whose genetic variability considerably affects disease manifestation, diagnosis and control, primarily pursued by vaccination. In Egypt, very virulent strains (genotype A3B2), responsible for typical IBD signs and lesions and high mortality, have historically prevailed. The present molecular survey, however, suggests that a major epidemiological shift might be occurring in the country. Out of twenty-four samples collected in twelve governorates in 2022-2023, seven tested positive for IBDV. Two of them were A3B2 strains related to other very virulent Egyptian isolates, whereas the remaining five were novel variant IBDVs (A2dB1b), reported for the first time outside of Eastern and Southern Asia. This emerging genotype spawned a large-scale epidemic in China during the 2010s, characterized by subclinical IBD with severe bursal atrophy and immunosuppression. Its spread to Egypt is even more alarming considering that, contrary to circulating IBDVs, the protection conferred by available commercial vaccines appears suboptimal. These findings are therefore crucial for guiding monitoring and control efforts and helping to track the spread of novel variant IBDVs, possibly limiting their impact.