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.

Molecular Survey on Porcine Parvoviruses (PPV1-7) and Their Association with Major Pathogens in Reproductive Failure Outbreaks in Northern Italy.

Successful reproductive performance is key to farm competitiveness in the global marketplace. Porcine parvovirus 1 (PPV1) has been identified as a major cause of reproductive failure, and since 2001 new species of porcine parvoviruses, namely PPV2-7, have been identified, although their role is not yet fully understood yet. The present study aimed to investigate PPVs' presence in reproductive failure outbreaks occurring in 124 farms of northern Italy. Fetuses were collected from 338 sows between 2019 and 2021 and tested for PPVs by real-time PCR-based assays and for other viruses responsible for reproductive disease. At least one PPV species was detected in 59.7% (74/124) of the tested farms. In order, PPV1, PPV5, PPV6, PPV7 and PPV4 were the most frequently detected species, whereas fewer detections were registered for PPV2 and PPV3. Overall, the new PPV2-7 species were detected in 26.6% (90/338) of the cases, both alone or in co-infections: PCV-2 (7.1%, 24/338), PCV-3 (8.2%, 28/338), and PRRSV-1 (6.2%, 21/338) were frequently identified in association with PPVs. Single PPVs detections or co-infections with other agents commonly responsible for reproductive failure should encourage future studies investigating their biological, clinical, and epidemiological role, for a better preparedness for potential emerging challenges in intensive pig production.

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.

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.

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.

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.

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.

Wild ungulates as sentinels of flaviviruses and tick-borne zoonotic pathogen circulation: an Italian perspective.

BACKGROUND: Vector-borne zoonotic diseases are a concerning issue in Europe. Lyme disease and tick-borne encephalitis virus (TBEV) have been reported in several countries with a large impact on public health; other emerging pathogens, such as Rickettsiales, and mosquito-borne flaviviruses have been increasingly reported. All these pathogens are linked to wild ungulates playing roles as tick feeders, spreaders, and sentinels for pathogen circulation. This study evaluated the prevalence of TBEV, Borrelia burgdorferi sensu lato, Rickettsia spp., Ehrlichia spp., and Coxiella spp. by biomolecular screening of blood samples and ticks collected from wild ungulates. Ungulates were also screened by ELISA and virus neutralization tests for flaviviral antibody detection. RESULTS: A total of 274 blood samples were collected from several wild ungulate species, as well as 406 Ixodes ricinus, which were feeding on them. Blood samples tested positive for B. burgdorferi s.l. (1.1%; 0-2.3%) and Rickettsia spp. (1.1%; 0-2.3%) and showed an overall flaviviral seroprevalence of 30.6% (22.1-39.2%): 26.1% (17.9-34.3%) for TBEV, 3.6% (0.1-7.1%) for Usutu virus and 0.9% (0-2.7%) for West Nile virus. Ticks were pooled when possible and yielded 331 tick samples that tested positive for B. burgdorferi s.l. (8.8%; 5.8-11.8%), Rickettsia spp. (26.6%; 21.8-31.2%) and Neoehrlichia mikurensis (1.2%; 0-2.4%). TBEV and Coxiella spp. were not detected in either blood or tick samples. CONCLUSIONS: This research highlighted a high prevalence of several tick-borne zoonotic pathogens and high seroprevalence for flaviviruses in both hilly and alpine areas. For the first time, an alpine chamois tested positive for anti-TBEV antibodies. Ungulate species are of particular interest due to their sentinel role in flavivirus circulation and their indirect role in tick-borne diseases and maintenance as Ixodes feeders and spreaders.

Wilder than intense: higher frequency, variability, and viral flows of porcine circovirus 3 in wild boars and rural farms compared to intensive ones in northern Italy.

Introduction: Porcine circovirus 3 (PCV-3) was firstly reported in 2017. Although evidence of its pathogenic role has been provided, its clinical relevance seems lower than Porcine circovirus 2 (PCV-2), as well as its evolutionary rate. Different studies have reported a high PCV-3 prevalence in wild boars, sometimes higher than the one observed in commercial pigs. Nevertheless, to date, few studies have objectively investigated the relationships between these populations when inhabiting the same area. Moreover, the role of small-scale, backyard pig production in PCV-3 epidemiology is still obscure. Methods: The present study investigated PCV-3 occurrence in 216 samples collected from the same area of Northern Italy from commercial and rural pigs, and wild boars. PCV-3 presence was tested by qPCR and complete genome or ORF2 sequences were obtained when possible and analysed using a combination of statistical, phylogenetic and phylodynamic approaches. Results: A higher infection risk in wild boars and rural pigs compared to the commercial ones was demonstrated. The phylodynamic analysis confirmed a larger viral population size in wild and rural populations and estimated a preferential viral flow from these populations to commercial pigs. A significant flow from wild to rural animals was also proven. The analysis of the Italian sequences and the comparison with a broader international reference dataset highlighted the circulation of a highly divergent clade in Italian rural pigs and wild boars only. Discussion: Overall, the present study results demonstrate the role of non-commercial pig populations in PCV-3 maintenance, epidemiology and evolution, which could represent a threat to intensive farming.

Feline Parvovirus Lethal Outbreak in a Group of Adult Cohabiting Domestic Cats.

Feline panleukopenia is a highly contagious and often fatal disease in cats. The virus, known as feline panleukopenia virus (FPV), primarily affects kittens and unvaccinated cats. It is transmitted through contact with infected cats or their bodily fluids, as well as contaminated objects and environments. The diagnosis of FPV infection can be confirmed through a combination of clinical signs, blood tests, and fecal testing. Prevention through vaccination is recommended for all cats. This case report describes an outbreak of feline panleukopenia in a group of unvaccinated domestic cats that resulted in acute mortality. The lesions were evaluated using histopathology, and the specific viral strain was characterized using molecular techniques. The clinical course of the outbreak was peracute, with a hemorrhagic pattern and 100% of lethality. The observed clinical-pathological pattern was unusual; nevertheless, molecular studies did not highlight peculiar genomic features of the parvovirus isolate. The outbreak affected 3 out of 12 cats in a very short time. However, the prompt application of biosecurity measures and vaccination resulted in an effective interruption of virus spread. In conclusion, we could assume that the virus found the ideal conditions to infect and replicate at high titers, resulting in a particularly aggressive outbreak.

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.

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.

Effect of changes of vaccination strategies on IBV epidemiology, diagnosis and control: an Italian retrospective study.

Infectious bronchitis virus (IBV) is among the most impactful poultry pathogens, whose control, based on biosecurity and routine vaccination, is hampered by the existence of countless genetic variants sharing poor cross­protection. A retrospective study was conducted on IBV positive samples collected in Italian broiler farms from 2012 to 2019. In 2015, the adopted vaccination protocol shifted from a Mass and 793B­based vaccines to the administration of Mass and QX vaccines, allowing to study how changes in vaccination strategies may affect IBV epidemiology, control and diagnosis in the field. The most frequently detected lineages were QX (70.3%), 793B (15.8%) and Mass (11.9%). The relative frequencies of QX and 793B detections remained stable throughout the study, while Mass detections significantly increased after the vaccination change. Rather than to an actual growth of Mass population size, this finding may be attributable to different vaccine interactions, with Mass strains being more frequently concealed by 793B vaccines than by QX ones. Based on the obtained results, the two vaccination protocols appear to be similarly effective in fighting IB outbreaks, which in the last decade have been caused primarily by QX field strains in Italy. These results indicate that vaccination strategies may significantly affect IBV epidemiology and diagnosis, and should therefore be considered when choosing and interpreting diagnostic assays and planning control measures.

Evaluation of UVC Excimer Lamp (222 nm) Efficacy for Coronavirus Inactivation in an Animal Model.

The current pandemic caused by severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has encouraged the evaluation of novel instruments for disinfection and lowering infectious pressure. Ultraviolet subtype C (UVC) excimer lamps with 222 nm wavelength have been tested on airborne pathogens on surfaces and the exposure to this wavelength has been considered safer than conventional UVC. To test the efficacy of UVC excimer lamps on coronaviruses, an animal model mimicking the infection dynamics was implemented. An attenuated vaccine based on infectious bronchitis virus (IBV) was nebulized and irradiated by 222 nm UVC rays before the exposure of a group of day-old chicks to evaluate the virus inactivation. A control group of chicks was exposed to the nebulized vaccine produced in the same conditions but not irradiated by the lamps. The animals of both groups were sampled daily and individually by choanal cleft swabs and tested usign a strain specific real time RT-PCR to evaluate the vaccine replication. Only the birds in the control group were positive, showing an active replication of the vaccine, revealing the efficacy of the lamps in inactivating the vaccine below the infectious dose in the other group.

Efficacy of live attenuated, vector and immune complex infectious bursal disease virus (IBDV) vaccines in preventing field strain bursa colonization: A European multicentric study.

Infectious bursal disease virus (IBDV) is among the most relevant and widespread immunosuppressive agents, which can severely damage poultry farming by causing direct losses, predisposing the host to secondary diseases and reducing the efficacy of vaccination protocols against other infections. IBDV has thus been the object of intense control activities, largely based on routine vaccination. However, the need for protecting animals from the infection in the first period of the production cycle, when the bursa susceptibility is higher, clashes with the blanketing effect of maternally derived antibodies. To overcome this issue, other strategies have been developed besides live attenuated vaccines, including vector vaccines and immune complex (icx) ones. The present study aims to investigate, in field conditions, the efficacy of these approaches in preventing IBDV infection in laying chickens vaccinated with either live attenuated, vector or immune complex (icx) vaccines. For this purpose, a multicentric study involving 481 farms located in 11 European countries was organized and IBDV infection diagnosis and strain characterization was performed at 6 weeks of age using a molecular approach. Vaccine strains were commonly detected in flocks vaccinated with live or icx vaccines. However, a significantly higher number of field strains (characterized as very virulent IBDVs) was detected in flocks vaccinated with vector vaccines, suggesting their lower capability of preventing bursal colonization. Different from vector vaccines, live and icx ones have a marked bursal tropism. It can thus be speculated that vaccine virus replication in these sites could limit vvIBDV replication by direct competition or because of a more effective activation of innate immunity. Although such different behavior doesn't necessarily affect clinical protection, further studies should be performed to evaluate if vvIBDV replication could still be associated with subclinical losses and/or for viral circulation in a "vaccinated environment" could drive viral evolution and favor the emergence of vaccine-escape variants.

Investigation of Carnivore protoparvovirus 1 and Amdoparvovirus infections in red fox populations of the Italian Dolomites.

Members of the family Parvoviridae are well recognized infectious agents of companion, livestock and wild animals as well, whose relevance on production, health, welfare and conservation is often high. Nevertheless, the knowledge of their epidemiology in wild populations is scarce or fragmentary. In this study, the presence and features of two parvoviruses, Carnivore protoparvovirus 1 and Amdoparvovirus, were evaluated in the red fox population resident in the Dolomites area, Northern Italy, and compared with the scenario of other countries and Italian regions. Six out of 117 spleen samples (5.13%: 95CI: 1.91-10.83%) tested positive to Carnivore protoparvovirus 1 and were molecularly characterized as Canine parvovirus (CPV). Infection frequency was comparable with that observed in wild carnivore populations present in Southern Italian regions, although in that case, Feline parvovirus (FPV) was predominant. No evidence of infection-related clinical signs was reported and viral loads were invariably low, suggesting the subclinical nature of the infection, the persistent carrier status or the detection of traces of viral DNA. No samples tested positive to Amdoparvovirus genus-specific PCR. The present study provides the first evidence of CPV circulation in the Northern Italy fox population. Unfortunately, the inevitable convenience nature of the sampling prevents definitive conclusions. Therefore, a more coordinated and standardized approach should be applied, at least in neighbouring geographic areas, to study these viral infections and their relevance in wildlife.

Viral subpopulation variability in different batches of Infectious bronchitis virus (IBV) vaccines based on GI-23 lineage: Implications for the field.

The control of infectious bronchitis (IB) is largely based on routine vaccine administration, often using live-attenuated vaccines. However, their capability to replicate and be transmitted among animals and farms implies significant risks. The detection of strains genetically related to vaccines complicates the diagnostic process and understanding of the viral molecular epidemiology. Moreover, reversion to virulence and associated clinical outbreaks can occur although the underlying mechanism are often unknown. In the present study, three vaccine vials, based on IBV GI-23 lineage (also known as Variant2) were deep sequenced through Next Generation Sequencing (NGS) to investigate the presence and features of viral subpopulations. To elucidate the consequences in the field and identify potential markers suitable for a DIVA strategy, the S1 sequences of strains originating from farms in different countries were sequenced and classified based on the knowledge of their vaccination history and similarity with the applied vaccine. Although all considered vaccine batches shared the same consensus sequence, different subpopulations were identified suggesting independent and poorly constrained evolutionary processes. When compared with strains sampled from farms, the vaccine consensus sequences and the respective subpopulations clustered with vaccine strains and no genetic features were consistently shared with field strains. Therefore, if vaccine-induced outbreaks occur, they are more likely to originate from in vivo evolution rather than selection of already present subpopulations. Although some amino acid residues were most commonly detected in field or vaccine strains, no consistent marker could be identified. The occurrence of subpopulations within IBV GI-23-based vaccines and variability featuring different production batches was demonstrated. Being such a phenomenon apparently driven by random genetic drift rather than directional selection, the differentiation between field and vaccine-derived strains appears extremely challenging based on sequence analysis alone. The knowledge of farm management and vaccination history should thus be considered for a proper epidemiological investigation.

Molecular Survey on A, B, C and New Avian Metapneumovirus (aMPV) Subtypes in Wild Birds of Northern-Central Italy.

Recent insights into the genetic and antigenic variability of avian metapneumovirus (aMPV), including the discovery of two new subtypes, have renewed interest in this virus. aMPV causes a well-known respiratory disease in poultry. Domestic species show different susceptibility to aMPV subtypes, whereas sporadic detections in wild birds have revealed links between epidemiology and migration routes. To explore the epidemiology of aMPV in wild species, a molecular survey was conducted on samples that were collected from wild birds during avian influenza surveillance activity in Italy. The samples were screened in pools by multiplex real time RT-PCR assays in order to detect and differentiate subtypes A, B, C, and those that have been newly identified. All the birds were negative, except for a mallard (Anas platyrhynchos) that was positive for aMPV subtype C (sampled in Padua, in the Veneto region, in 2018). The sequencing of partial M and full G genes placed the strain in an intermediate position between European and Chinese clusters. The absence of subtypes A and B supports the negligible role of wild birds, whereas subtype C detection follows previous serological and molecular identifications in Italy. Subtype C circulation in domestic and wild populations emphasizes the importance of molecular test development and adoption to allow the prompt detection of this likely emerging subtype.

Phylodynamic and phylogeographic reconstruction of porcine reproductive and respiratory syndrome virus (PRRSV) in Europe: Patterns and determinants.

Porcine reproductive and respiratory syndrome (PRRS) is among the most devastating diseases affecting the pig industry. Despite vaccines having been available for decades, the remarkable genetic variability of this virus, leading to poor cross-protection, has limited their efficacy, and other measures must be adopted to effectively control the viral circulation. Some recent studies have investigated the factors involved in viral spreading and persistence, at least at the local level. However, despite the topic's relevance, no statistically grounded evidence is currently available evaluating the variables more involved in porcine reproductive and respiratory syndrome virus (PRRSV) epidemiological success at a broader scale, such as the European scale. In the present study, an extensive phylodynamic and phylogeographic analysis was performed on more than 1000 ORF5 sequences to investigate the history, dynamics and spreading patterns of PRRSV within European borders. Moreover, several potential predictors, representative of swine population features and trade, human population, economy and geographic characteristics, were evaluated through a specifically designed generalized linear model (GLM) to assess their weight on viral migration rate between countries over time. Although pig stock density, mean PRRSV strain genetic diversity, investments in agriculture (including a likely role of vaccination) and farmer education were involved to a certain extent, the major determinant was proven to be by far the live pig trade. Providing a robust depiction of PRRSV European molecular epidemiology patterns and determinants, the present study could contribute to a more rational allocation of limited resources based on an effective prioritization of control measures.

Molecular Survey and Identification of Campylobacter spp. in Layer Farms in Central Ethiopia.

Few data are available on Campylobacter spp. presence in chickens in Ethiopia. Due to its importance for both the poultry sector and public health, a sampling activity was planned to evaluate Campylobacter spp. presence in layer farms in Bishoftu and Mojo, Central Ethiopia. Twenty cloacal pooled samples were collected and tested with molecular assays for detection and Sanger-sequenced for species identification. As a secondary aim, samples were also tested for Salmonella spp. by PCR, and all samples were negative. On the other hand, 70% of cloacal swab pools were positive for Campylobacter spp.: 71.4% of the positive samples belonged to C. jejuni species, 21.4% to C. avium and 7.1% to C. helveticus. Campylobacter spp. was identified in almost all farms regardless of farm and flock size, age and hybrid types of the birds and antimicrobial treatment. Campylobacter jejuni is a common finding in chickens, whereas species such as C. avium and C. helveticus were newly reported in Ethiopia, revealing a variability that needs to be monitored in light of the public health significance of this pathogen.