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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. [ABSTRACT FROM AUTHOR]

Simple Summary: Avian metapneumovirus (aMPV) causes substantial economic losses globally. Different aMPV subtypes circulate in various regions, with subtypes A and B prevalent in the Old World and aMPV-C in North America. Recently, aMPV-A and aMPV-B have been detected in the U.S., raising questions about their introduction pathways. This study used phylodynamic and phylogeographic analyses of the G protein sequences to investigate potential importation routes. Findings suggest that aMPV-B in the U.S. likely originated from Eastern Asian strains related to European ones, with wild bird migration through the Beringian crucible being a probable pathway, similarly to avian influenza. aMPV-A appears to have Mexican origins, with strains related to Asian ones, pointing again to wild bird migration rather than trade or illegal importation. Given the limited information on wild birds' role in aMPV spread and the significant impact on the poultry industry, further wild bird surveys are recommended. 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Simple Summary: The present study demonstrates the role of intensive poultry production in the rise of fowl adenovirus (FAdV), similar to what occurred for several multifactorial viral diseases of livestock. Although effective in limiting viral circulation, the applied control strategies, likely shaped its evolution. In fact, after the development and application of FAdV vaccines, an increase in evolutionary rate was observed and several sites and regions of the Hexon protein were proven under a significant pervasive or episodic diversifying selection, especially those exposed on the viral surface and target of the host response. The notion that FAdV has increased in relevance in the last years could thus be a misleading perception related to an increased diagnostic capability and awareness of the topic. Alternatively, a limited number of flocks could be more severely affected because of the waning population immunity. Further efforts should be devoted to the acquisition of more molecular data on other geographic regions and FAdV species, also to assess the representativeness of the present results on a broader scale. 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. [ABSTRACT FROM AUTHOR]

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 noncommercial pig populations in PCV-3 maintenance, epidemiology and evolution, which could represent a threat to intensive farming. [ABSTRACT FROM AUTHOR]

Simple Summary: 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 related to 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 of animal infectious diseases and zoonoses. 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")—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. The present work reviews the application of sensor technologies, specifically, the principles and benefits of advanced statistical techniques and their use in developing effective and reliable classification and prediction models to benefit the farming system. Finally, recent progress in pathogen genome sequencing and analysis is discussed, highlighting practical applications in epidemiological tracking and control strategies. 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. [ABSTRACT FROM AUTHOR]

Porcine circovirus type 2 (PCV2) is one of the most relevant infectious agents affecting domestic pigs. Recently, a surprising PCV2 genetic heterogenicity has been reported in Africa. Nevertheless, the knowledge of the epidemiology of PCV2 in African countries, in both domestic and wild species, is limited and sparse. Having this in mind, in the present study, the PCV2 circulation and its molecular epidemiology in Southwestern Ethiopia have been investigated by collecting 64 samples from domestic pigs, wild boars, and warthogs. PCV2 genome presence was detected and quantified using qPCR and ORF2 sequencing was attempted on positive samples. Ten samples, 8 wild boars, 1 domestic pig, and 1 warthog, tested PCV2 positive. Complete ORF2 sequences were obtained from 5 wild boars; 4 of those were classified as PCV2d and 1 as PCV2b. Both PCV2b and PCV2d were related to strains of Asian origin, most commonly from China. The role of this country in the exportation of PCV2 strains in Ethiopia, and Africa in general, might be supported by the crescent economic relationship between the two continents. The obtained evidence also testifies to the inadequacy and/or poor application of biosecurity measures separating wild and domestic animals. Further, extensive and systematic studies should be performed to more deeply characterize the molecular epidemiology of PCV2 in this region, in order to improve our understanding of these ecological niches in the evolution and dispersal of PCV2. [ABSTRACT FROM AUTHOR]

Four porcine circoviruses (PCVs) have been discovered over time and seem to share a common history, particularly for PCV‐2 and ‐3. Despite being reported as apparently new viruses, rapidly emerging as a threat for the worldwide swine industry, they were then proven to have been circulating and coexisting with domestic pigs undetected for decades, without causing relevant health issues. A similar scenario could be true for the most recently identified PCV‐4. However, its detection in Asia only and the limited genetic variability could suggest a truly recent origin. To investigate which of the above‐mentioned scenarios is more plausible, a phylodynamic analysis was performed on all available PCV‐4 sequences for which adequate metadata were available to reconstruct the viral history and evolution. Obtained results suggest an ancient origin, at least decades ago, followed by a prolonged low‐level circulation and a moderate increase in viral population size after the second half of the XX century, in parallel with a progressive rise in pig population and farming intensification. A relevant local geographical clustering was also highlighted. The reason behind such low spreading capacity and limited geographical distribution compared to other circoviruses is currently obscure and will require dedicated studies, involving a more extensive sampling and sequencing activity. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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.

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.