CamTrapAsia: A dataset of tropical forest vertebrate communities from 239 camera trapping studies.

Information on tropical Asian vertebrates has traditionally been sparse, particularly when it comes to cryptic species inhabiting the dense forests of the region. Vertebrate populations are declining globally due to land-use change and hunting, the latter frequently referred as "defaunation." This is especially true in tropical Asia where there is extensive land-use change and high human densities. Robust monitoring requires that large volumes of vertebrate population data be made available for use by the scientific and applied communities. Camera traps have emerged as an effective, non-invasive, widespread, and common approach to surveying vertebrates in their natural habitats. However, camera-derived datasets remain scattered across a wide array of sources, including published scientific literature, gray literature, and unpublished works, making it challenging for researchers to harness the full potential of cameras for ecology, conservation, and management. In response, we collated and standardized observations from 239 camera trap studies conducted in tropical Asia. There were 278,260 independent records of 371 distinct species, comprising 232 mammals, 132 birds, and seven reptiles. The total trapping effort accumulated in this data paper consisted of 876,606 trap nights, distributed among Indonesia, Singapore, Malaysia, Bhutan, Thailand, Myanmar, Cambodia, Laos, Vietnam, Nepal, and far eastern India. The relatively standardized deployment methods in the region provide a consistent, reliable, and rich count data set relative to other large-scale pressence-only data sets, such as the Global Biodiversity Information Facility (GBIF) or citizen science repositories (e.g., iNaturalist), and is thus most similar to eBird. To facilitate the use of these data, we also provide mammalian species trait information and 13 environmental covariates calculated at three spatial scales around the camera survey centroids (within 10-, 20-, and 30-km buffers). We will update the dataset to include broader coverage of temperate Asia and add newer surveys and covariates as they become available. This dataset unlocks immense opportunities for single-species ecological or conservation studies as well as applied ecology, community ecology, and macroecology investigations. The data are fully available to the public for utilization and research. Please cite this data paper when utilizing the data.

Detection of Chlamydia psittaci in the Genital Tract of Horses and in Environmental Samples: A Pilot Study in Sardinia.

The members of the Chlamydiaceae family are important pathogens that infect a wide range of vertebrate hosts, including humans. Among them, Chlamydia psittaci, historically considered as an avian agent, has recently been identified in livestock, primarily sheep and cattle, but also in horses, with the infection being linked to reproductive disorders, such as abortion, absorption of embryos, stillbirth, and the birth of weak foals. Much less is known about chlamydial infections in the Sardinian equine population. This study aimed to identify the chlamydial diversity in genital samples from asymptomatic Sardinian horses. However, some horses had a previous history of reproductive disorders, i.e., abortion and infertility. A total of 60 horses (39 mares and 21 stallions) were opportunistically recruited from 17 equine farms in central-northern Sardinia. Vaginal and uterine swabs from mares and urethral swabs and seminal fluid from stallions were sampled for the presence of chlamydial DNA. Samples from environments where the horses lived were also tested for the detection of Chlamydia spp. Eight vaginal swabs (8/39; 20%), two uterine swabs (2/27; 7%), two seminal fluid samples (2/20; 10%), and one urethral swab (1/21; 4.7%) were found to be positive for Chlamydia spp. by PCR analysis. In addition, results from environmental samples showed the presence of Chlamydia spp. in three environmental swabs (3/8; 37.5%) and five water samples (5/16; 31.2%). Sequencing results revealed that strains here identified were 99-100% similar to members belonging to the Chlamydiaceae family, including C. abortus, C. psittaci, and uncultured Chlamydia genotypes. ompA species-specific PCR performed on samples was found to be positive after 16S rRNA amplification gave positive results for C. psittaci. These results reveal the first presence of C. psittaci in the genital tract of horses and in the environment in Sardinia and indicate that this pathogen could be the prevailing cause of infertility and abortion in the tested equines. However, these findings need further proof and highlight the importance of adopting a 'One Health' approach to control the presence of this zoonotic bacteria in domestic animals in order to understand its impact on people exposed to the infection risk.

Passive Surveillance as a Key Tool for African Swine Fever Eradication in Wild Boar: A Protocol to Find Carcasses Tested and Validated in the Mediterranean Island of Sardinia.

African swine fever (ASF) is one of the most important and serious contagious hemorrhagic viral diseases affecting domestic pigs and wild boar and is associated with high mortality rates while also having an extensive sanitary and socioeconomic impact on the international trade of animal and swine products. The early detection of the disease is often hampered by inadequate surveillance. Among the surveillance strategies used, passive surveillance of wild boars is considered the most effective method for controlling the African swine fever virus (ASFV). Otherwise, the design of a sufficiently sensitive ASF surveillance system requires a solid understanding of the epidemiology related to the local eco-social context, especially in the absence of virus detection. Even if the number of carcasses needed to demonstrate ASF eradication has been established, the scientific context lacks detail compared to protocols applied in the active search for wild boar carcasses. The aim of this study was to describe the protocol applied in the active search for carcasses, providing detailed information on the number of people and dogs as well as the amount of time and space used within the Mediterranean area. Using a specific tool developed to record, trace, and share field data (the GAIA observer app), a total of 33 active searches for wild boar carcasses were organized during 2021-2023. Most of these searches were planned to find carcasses that had previously been reported by hunters. A total of 24 carcasses were found, with only 2 carcasses not previously reported. The final protocol applied involved four people, with an average speed of 1.5 km/h. When a carcass had been previously reported, about 2 km of distance had to be covered in about 1.5 h to find the carcass, and even less time was spent when a dog (untrained) was present. In conclusion, it can be stated that, when searching for carcasses, solid collaboration with local hunters or other forest visitors is necessary to ensure carcasses are reported. The process involves small groups of experts actively searching for carcasses, possibly with the use of hunting dogs without special training. The data presented could be of valid support for those countries characterized by Mediterranean vegetation that are faced with the need to plan active carcass searches.

Echocardiographic heart ageing patterns predict cardiovascular and non-cardiovascular events and reflect biological age: the SardiNIA study.

AIMS: Age is a crucial risk factor for cardiovascular (CV) and non-CV diseases. As people age at different rates, the concept of biological age has been introduced as a personalized measure of functional deterioration. Associations of age with echocardiographic quantitative traits were analysed to assess different heart ageing rates and their ability to predict outcomes and reflect biological age. METHODS AND RESULTS: Associations of age with left ventricular mass, geometry, diastolic function, left atrial volume, and aortic root size were measured in 2614 healthy subjects. Based on the 95% two-sided tolerance intervals of each correlation, three discrete ageing trajectories were identified and categorized as 'slow', 'normal', and 'accelerated' heart ageing patterns. The primary endpoint included fatal and non-fatal CV events, and the secondary endpoint was a composite of CV and non-CV events and all-cause death. The phenotypic age of the heart (HeartPhAge) was estimated as a proxy of biological age. The slow ageing pattern was found in 8.7% of healthy participants, the normal pattern in 76.9%, and the accelerated pattern in 14.4%. Kaplan-Meier curves of the heart ageing patterns diverged significantly (P = 0.0001) for both primary and secondary endpoints, with the event rate being lowest in the slow, intermediate in the normal, and highest in the accelerated pattern. In the Cox proportional hazards model, heart ageing patterns predicted both primary (P = 0.01) and secondary (P = 0.03 to <0.0001) endpoints, independent of chronological age and risk factors. Compared with chronological age, HeartPhAge was 9 years younger in slow, 4 years older in accelerated (both P < 0.0001), and overlapping in normal ageing patterns. CONCLUSION: Standard Doppler echocardiography detects slow, normal, and accelerated heart ageing patterns. They predict CV and non-CV events, reflect biological age, and provide a new tool to calibrate prevention timing and intensity.

Age is the main risk factor for cardiovascular (CV) disease. Since people age and develop diseases at very different rates, biological age has been proposed as a more accurate measure of the body's functional decline. This study aimed to investigate the ageing rates of the heart and to assess their impact on CV events. The phenotypic age of the heart was also estimated as a proxy for biological age. Associations of age with Doppler echocardiographic parameters were analysed in a subgroup of 2614 clinically healthy subjects, part of a larger cohort of 3817 adults of both sexes.Three patterns of slow, normal, and accelerated ageing rates of the heart were detected. They predicted both CV and non-CV events, with different and progressively increasing event rates from the slow to the accelerated pattern. Compared with chronological age, the phenotypic (biological) age of the heart was 9 years younger in the slow pattern, 4 years older in the accelerated pattern, and comparable in the normal pattern.A standard Doppler echocardiogram is therefore able to detect three distinct heart ageing patterns, which reflect different biological susceptibilities to age-dependent diseases and provide a new tool for personalizing timeliness and intensity of prevention.

The illegal rearing and slaughtering of pigs in the wild on the Mediterranean island of Sardinia favor an increase in the biomass of Trichinella britovi in wild boars (Sus scrofa) but do not affect the serological prevalence of infection.

BACKGROUND: Worms of the nematode genus Trichinella are zoonotic pathogens with a worldwide distribution. The first report of Trichinella on the Mediterranean island of Sardinia was for Trichinella britovi, one of the four species of this genus circulating in Europe, which was identified in 2005 following an outbreak of trichinellosis in humans due to the consumption of pork from pigs reared in the wild. Since then, T. britovi larvae have been repeatedly isolated from free-ranging pigs, foxes (Vulpes vulpes) and wild boars (Sus scrofa) sampled in the central-eastern region of the island (Orgosolo municipality), but have never been isolated from samples from other areas of the island. The aim of this study was to investigate the parasitological and serological prevalence of T. britovi infection in wild boars in Sardinia over space [eight wild boar hunting management units (HMUs)] and time (seven wild boar hunting seasons). METHODS: Muscle and serum samples of boars killed in the 2014-2015 to 2020-2121 hunting seasons were collected from eight HMUs of central and south-western Sardinia. Trichinella sp. larvae were detected by artificial digestion of predilection muscles. A total of 4111 serum samples of wild boar were collected from the investigated HMUs and tested by enzyme-linked immunosorbent assay as a screening test and by western blot as a confirmatory test using excretory/secretory antigens. RESULTS: Trichinella britovi muscle larvae were detected in six (0.03%) of the 17,786 wild boars tested. All of the Trichinella sp.-positive wild boars had been hunted in Orgosolo municipality (central-eastern area of the island), except for one, hunted in a neighboring municipality. An overall serological prevalence of 3.8% (95% confidence interval, 3.3-4.5) was detected by western blot. No statistical differences were detected between the HMUs where T. britovi larvae were detected in wild boars, foxes, and free-ranging pigs and those where wild boars, foxes and free-ranging pigs tested negative. CONCLUSIONS: The serological prevalence did not vary between the wild boar populations in which the larval load was detectable by artificial digestion (Orgosolo municipality) and those in which the larval load was below the detection limit. Furthermore, the serological prevalence of anti-Trichinella immunoglobulin G in the wild boar populations remained constant during the study period, which covered seven wild boar hunting seasons. As the transmission events (i.e., the serological prevalence) are stable, the high biomass of the parasite in Orgosolo municipality can only have arisen as a consequence of factors independent of its natural cycle, i.e., the presence of a high number of free-ranging pigs, and the concomitant presence of African swine fever, due to illegal pig slaughtering in the field. This epidemiological situation suggests that the natural cycle of T. britovi may be influenced by inappropriate pig husbandry and slaughtering practices.

Estimating the Directional Spread of Epidemics in Their Early Stages Using a Simple Regression Approach: A Study on African Swine Fever in Northern Italy.

The early identification of the spreading patterns of an epidemic infectious disease is an important first step towards the adoption of effective interventions. We developed a simple regression-based method to estimate the directional speed of a disease's spread, which can be easily applied with a limited dataset. We tested the method using simulation tools, then applied it on a real case study of an African Swine Fever (ASF) outbreak identified in late 2021 in northwestern Italy. Simulations showed that, when carcass detection rates were <0.1, the model produced negatively biased estimates of the ASF-affected area, with the average bias being about -10%. When detection rates were >0.1, the model produced asymptotically unbiased and progressively more predictable estimates. The model produced rather different estimates of ASF's spreading speed in different directions of northern Italy, with the average speed ranging from 33 to 90 m/day. The resulting ASF-infected areas of the outbreak were estimated to be 2216 km2, about 80% bigger than the ones identified only thorough field-collected carcasses. Additionally, we estimated that the actual initial date of the ASF outbreak was 145 days earlier than the day of first notification. We recommend the use of this or similar inferential tools as a quick, initial way to assess an epidemic's patterns in its early stages and inform quick and timely management actions.

Epizootic Hemorrhagic Disease Virus Serotype 8, Italy, 2022.

We describe the detection of epizootic hemorrhagic disease virus (EHDV) serotype 8 in cattle farms in Sardinia and Sicily in October-November 2022. The virus has a direct origin in North Africa; its genome is identical (>99.9% nucleotide sequence identity) to EHDV serotype 8 strains detected in Tunisia in 2021.

Origin, Genetic Variation and Molecular Epidemiology of SARS-CoV-2 Strains Circulating in Sardinia (Italy) during the First and Second COVID-19 Epidemic Waves.

Understanding how geography and human mobility shape the patterns and spread of infectious diseases such as COVID-19 is key to control future epidemics. An interesting example is provided by the second wave of the COVID-19 epidemic in Europe, which was facilitated by the intense movement of tourists around the Mediterranean coast in summer 2020. The Italian island of Sardinia is a major tourist destination and is widely believed to be the origin of the second Italian wave. In this study, we characterize the genetic variation among SARS-CoV-2 strains circulating in northern Sardinia during the first and second Italian waves using both Illumina and Oxford Nanopore Technologies Next Generation Sequencing methods. Most viruses were placed into a single clade, implying that despite substantial virus inflow, most outbreaks did not spread widely. The second epidemic wave on the island was actually driven by local transmission of a single B.1.177 subclade. Phylogeographic analyses further suggest that those viral strains circulating on the island were not a relevant source for the second epidemic wave in Italy. This result, however, does not rule out the possibility of intense mixing and transmission of the virus among tourists as a major contributor to the second Italian wave.

The Long-Jumping of African Swine Fever: First Genotype II Notified in Sardinia, Italy.

African swine fever (ASF) is a devastating infectious disease of domestic pigs and wild boar that is spreading quickly around the world and causing huge economic losses. Although the development of effective vaccines is currently being attempted by several labs, the absence of globally recognized licensed vaccines makes disease prevention and early detection even more crucial. ASF has spread across many countries in Europe and about two years ago affected the Italian susceptible population. In Italy, the first case of ASF genotype II in wild boar dates back to January 2022, while the first outbreak in a domestic pig farm was notified in August 2023. Currently, four clusters of infection are still ongoing in northern (Piedmont-Liguria and Lombardy), central (Lazio), and southern Italy (Calabria and Campania). In early September 2023, the first case of ASFV genotype II was detected in a domestic pig farm in Sardinia, historically affected by genotype I and in the final stage of eradication. Genomic characterization of p72, p54, and I73R/I329L genome regions revealed 100% similarity to those obtained from isolates that have been circulating in mainland Italy since January 2022 and also with international strains. The outbreak was detected and confirmed due to the passive surveillance plan on domestic pig farms put in place to provide evidence on genotype I's absence. Epidemiological investigations suggest 24 August as the most probable time of ASFV genotype II's arrival in Sardinia, likely due to human activities.

Estimation of R0 for the Spread of the First ASF Epidemic in Italy from Fresh Carcasses.

After fifty years of spread in the European continent, the African swine fever (ASF) virus was detected for the first time in the north of Italy (Piedmont) in a wild boar carcass in December, 2021. During the first six months of the epidemic, the central role of wild boars in disease transmission was confirmed by more than 200 outbreaks, which occurred in two different areas declared as infected. The virus entered a domestic pig farm in the second temporal cluster identified in the center of the country (Lazio). Understanding ASF dynamics in wild boars is a prerequisite for preventing the spread, and for designing and applying effective surveillance and control plans. The aim of this work was to describe and evaluate the data collected during the first six months of the ASF epidemic in Italy, and to estimate the basic reproduction number (R0) in order to quantify the extent of disease spread. The R0 estimates were significantly different for the two spatio-temporal clusters of ASF in Italy, and they identified the two infected areas based on the time necessary for the number of cases to double (td) and on an exponential decay model. These results (R0 = 1.41 in Piedmont and 1.66 in Lazio) provide quantitative knowledge on the epidemiology of ASF in Italy. These parameters could represent a fundamental tool for modeling country-specific ASF transmission and for monitoring both the spread and sampling effort needed to detect the disease early.

Changes in Estimating the Wild Boar Carcasses Sampling Effort: Applying the EFSA ASF Exit Strategy by Means of the WBC-Counter Tool.

African swine fever (ASF) is a devastating disease, resulting in the high mortality of domestic and wild pigs, spreading quickly around the world. Ensuring the prevention and early detection of the disease is even more crucial given the absence of licensed vaccines. As suggested by the European Commission, those countries which intend to provide evidence of freedom need to speed up passive surveillance of their wild boar populations. If this kind of surveillance is well-regulated in domestic pig farms, the country-specific activities to be put in place for wild populations need to be set based on wild boar density, hunting bags, the environment, and financial resources. Following the indications of the official EFSA opinion 2021, a practical interpretation of the strategy was implemented based on the failure probabilities of wrongly declaring the freedom of an area even if the disease is still present but undetected. This work aimed at providing a valid, applicative example of an exit strategy based on two different approaches: the first uses the wild boar density to estimate the number of carcasses need to complete the exit strategy, while the second estimates it from the number of wild boar hunted and tested. A practical free access tool, named WBC-Counter, was developed to automatically calculate the number of needed carcasses. The practical example was developed using the ASF data from Sardinia (Italian island). Sardinia is ASF endemic from 43 years, but the last ASFV detection dates back to 2019. The island is under consideration for ASF eradication declaration. The subsequent results provide a practical example for other countries in approaching the EFSA exit strategy in the best choices for its on-field application.

Evaluation of the microbiological and chemical aspects of autochthonous wild snails in Sardinia.

This study was conducted to acquire knowledge on the epidemiology and ecology of some zoonotic agents in snails. Chemical and microbiological analysis was carried out on 46 samples of snails belonging to the species of Helix aspersa and Helix (Eobania) vermiculata. The association between heavy metals and wild snails, a native consumer product in the Region of Sardinia, was determined. The molecular characterisation of Listeria monocytogenes virulence genes has shown a genetic profile that deserves more attention for the improvement of surveillance and risk prevention. Specimens of H. vermiculata showed higher concentrations of cadmium (M=0.80±0.56 mg/kg) than H. aspersa (M=0.61±0.17 mg /kg). A further objective was to determine whether the samples showed significant differences from the point of view of secretion characterisation, in terms of protein content, and to identify species-specific correlations and possible relationships with the environment. The presence of Salmonella enterica sub.sp houtenae (6,14: z4, z23) and Salmonella enterica subsp diarizonae (47: k: e, n, z15) (1 sample), Listeria monocytogenes (2 samples) with Molecular characterization of virulence genes together with the measurement of heavy metals in samples of wild snails has shown a health and hygiene profile that would deserve greater attention for the improvement of the surveillance and prevention of microbiological and chemical risk in such products which currently show a tendency towards increase in consumption.

Entomological Investigation of the Main Entomatic Adversities for Terrestrial Gastropods Helix aspersa Müller (Mollusca Gastropoda Pulmonata): A Preliminary Study in Sardinian Heliciculture Farms.

In the years 2020-2022, a survey was carried out with the aim of controlling the entomofauna present in seven Sardinian snail farms. The sampling was carried out during the spring-summer and autumn-winter periods, corresponding to the production cycles of the Helix aspersa snails (Müller, 1774), the species most frequently bred in snail farms. The samples were taken from farms located in different areas of the region. For the predatory species found in most of the farms, 38% of the individuals were of the Silpha tristis Illiger, 1798 (Coleoptera: Silphidae) species, 32% were Ocypus olens Müller, 1764 (Coleoptera: Staphylinidae), and 24% were Carabus (Macrothorax) morbillosus constantinus Kraatz, 1899 (Coleoptera: Carabidae). The Lampyris sardiniae Geisthardt, 1987 (Coleoptera: Lampyridae) and Licinus punctatulus Fabricius, 1792 (Coleoptera: Carabidae) species were equally detected in 3% of the farms. In some farms, the predatory species S. tristis and C.morbillosus costantinus had caused the death of several snails. This preliminary study aimed to provide a first evaluation and description of the critical issues facing the snails present in seven Sardinian snail farms. First, a specific survey of the entomofauna during two observational periods (i.e., the spring-summer and autumn-winter periods) was conducted. Context-specific description and evaluation will allow providing valid information for Italian and European heliciculture farms to ensure the well-being of the mollusks. The presence of predatory species in snail farms is not easy to control, but some precautions could be useful to avoid massive colonization.

Environmental Contamination by Echinococcus spp. Eggs as a Risk for Human Health in Educational Farms of Sardinia, Italy.

Cystic Echinococcosis (CE) is a severe zoonosis caused by the larval stage of the tapeworm Echinococcus granulosus. These parasites are naturally transmitted between canid definitive hosts that harbour the adult stage in the intestine, and mainly ungulate intermediate hosts, with larval cysts developing in their internal organs. The close coexistence between dog and sheep with incorrect hygiene management are the most important factors for the persistence of this parasitic pathology. The Educational Farms (EF) are farms and agritourisms suitably equipped to carry out training activities for people interested in farm practices and agricultural processing, in particular student groups. Public attendance of farms represents a new potential risk factor for the zoonoses transmission. Consumption of contaminated food and water in combination with contact or playing with domestic dogs (Canis familiaris) are possible routes of zoonoses human infection. In fact, Echinococcus spp. eggs may persist in the environment up to several months at low temperatures and moist conditions, having the chance of contaminating different matrices and surfaces. The aim of this investigation was to study environmental contamination by parasitic elements as a risk for zoonoses, such as Echinococcus spp. A total of 116 samples (35 of water, 33 of soil, 23 of vegetables, 25 of dog faeces) were collected in 30 EF in Sardinia. Samples were subjected to biomolecular investigation for the research of specific gene sequences of Echinococcus granulosus, Echinococcus multilocularis and Taenia spp. The study allowed to identify eight positive EF due to the presence of Echinococcusgranulosus in eight dog faeces samples and one positive EF due to the presence of Taenia spp. in a water sample. The work has allowed to develop and harmonise the diagnostic methods and operating protocols essential for controlling the spread of the CE to create "One Health" intervention plans in high endemic areas through the implementation of SOP (standard operating procedures) for monitoring the pathology in animals, humans and environment.

Effect of Different Disease-Modifying Therapies on Humoral Response to BNT162b2 Vaccine in Sardinian Multiple Sclerosis Patients.

Objectives: Vaccination against COVID-19 is highly recommended to patients affected by multiple sclerosis (MS); however, the impact of MS disease-modifying therapies (DMTs) on the immune response following vaccination has been only partially investigated. Here, we aimed to elucidate the effect of DMTs on the humoral immune response to mRNA-based anti-SARS-CoV-2 vaccines in MS patients. Methods: We obtained sera from 912 Sardinian MS patients and 63 healthy controls 30 days after the second dose of BNT162b2 vaccine and tested them for SARS-CoV-2 response using anti-Spike (S) protein-based serology. Previous SARS-CoV-2 infection was assessed by anti-Nucleocapsid (N) serology. Patients were either untreated or undergoing treatment with a total of 13 different DMTs. Differences between treatment groups comprised of at least 10 patients were assessed by generalized linear mixed-effects model. Demographic and clinical data and smoking status were analyzed as additional factors potentially influencing humoral immunity from COVID-19 vaccine. Results: MS patients treated with natalizumab, teriflunomide, azathioprine, fingolimod, ocrelizumab, and rituximab showed significantly lower humoral responses compared to untreated patients. We did not observe a statistically significant difference in response between patients treated with the other drugs (dimethyl fumarate, interferon, alemtuzumab and glatiramer acetate) and untreated patients. In addition, older age, male sex and active smoking were significantly associated with lower antibody titers against SARS-CoV-2. MS patients previously infected with SARS-CoV-2 had significantly higher humoral responses to vaccine than uninfected patients. Conclusion: Humoral response to BNT162b2 is significantly influenced by the specific DMTs followed by patients, as well as by other factors such as previous SARS-CoV-2 infection, age, sex, and smoking status. These results are important to inform targeted strategies to prevent clinically relevant COVID-19 in MS patients.

First Genomic Evidence of Dual African Swine Fever Virus Infection: Case Report from Recent and Historical Outbreaks in Sardinia.

African swine fever virus (ASFV) is one of the pathogens of highest concern worldwide. Despite different virus lineages co-circulating in several areas, dual infections in the same animal have been rarely observed, suggesting that ASF superinfections are infrequent events. Here we present the first genome-wide detection and analysis of two intragenotype dual ASFV infections. The dual infections have been detected in a hunted wild boar and in a pig carcass, both infected by ASFV genotype I in Sardinia in 1984 and 2018, respectively. We characterize the genetic differences between the two sequences, their intra-host frequency, and their phylogenetic relationship among fully sequenced ASFV strains from Sardinia. Both dual infections involve pairs of closely related but different viruses that were circulating in Sardinia in the same period. The results imply that dual ASFV infections or similar ASFV strains are more common than expected, especially in ASF endemic areas, albeit difficult to detect.

A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

African swine fever virus (ASFV) is the etiological agent of the devastating disease African swine fever (ASF), for which there is currently no licensed vaccine or treatment available. ASF is defined as one of the most serious animal diseases identified to date, due to its global spread in regions of Africa, Europe and Asia, causing massive economic losses. On the Italian island of Sardinia, the disease has been endemic since 1978, although the last control measures put in place achieved a significant reduction in ASF, and the virus has been absent from circulation since April 2019. Like many large DNA viruses, ASFV mutates at a relatively slow rate. However, the limited availability of whole-genome sequences from spatial-localized outbreaks makes it difficult to explore the small-scale genetic structure of these ASFV outbreaks. It is also unclear if the genetic variability within outbreaks can be captured in a handful of sequences, or if larger sequencing efforts can improve phylogenetic reconstruction and evolutionary or epidemiological inference. The aim of this study was to investigate the phylogenetic patterns of ASFV outbreaks between 1978 and 2018 in Sardinia, in order to characterize the epidemiological dynamics of the viral strains circulating in this Mediterranean island. To reach this goal, 58 new whole genomes of ASFV isolates were obtained, which represents the largest ASFV whole-genome sequencing effort to date. We provided a complete description of the genomic diversity of ASFV in terms of nucleotide mutations and small and large indels among the isolates collected during the outbreaks. The new sequences capture more than twice the genomic and phylogenetic diversity of all the previously published Sardinian sequences. The extra genomic diversity increases the resolution of the phylogenetic reconstruction, enabling us to dissect, for the first time, the genetic substructure of the outbreak. We found multiple ASFV subclusters within the phylogeny of the Sardinian epidemic, some of which coexisted in space and time.

African Swine Fever in Smallholder Sardinian Farms: Last 10 Years of Network Transmission Reconstruction and Analysis.

African swine fever (ASF) is a viral disease of suids that frequently leads to death. There are neither licensed vaccines nor treatments available, and even though humans are not susceptible to the disease, the serious socio-economic consequences associated with ASF have made it one of the most serious animal diseases of the last century. In this context, prevention and early detection play a key role in controlling the disease and avoiding losses in the pig value chain. Target biosecurity measures are a strong strategy against ASF virus (ASFV) incursions in farms nowadays, but to be efficient, these measures must be well-defined and easy to implement, both in commercial holdings and in the backyard sector. Furthermore, the backyard sector is of great importance in low-income settings, mainly for social and cultural practices that are highly specific to certain areas and communities. These contexts need to be addressed when authorities decide upon the provisions that should be applied in the case of infection or decide to combine them with strict preventive measures to mitigate the risk of virus spread. The need for a deeper understanding of the smallholder context is essential to prevent ASFV incursion and spread. Precise indications for pig breeding and risk estimation for ASFV introduction, spread and maintenance, taking into account the fact that these recommendations would be inapplicable in some contexts, are the keys for efficient target control measures. The aim of this work is to describe the 305 outbreaks that occurred in domestic pigs in Sardinia during the last epidemic season (2010-2018) in depth, providing essential features associated with intensive and backyard farms where the outbreaks occurred. In addition, the study estimates the average of secondary cases by kernel transmission network. Considering the current absence of ASF outbreaks in domestic pig farms in Sardinia since 2018, this work is a valid tool to specifically estimate the risk associated with different farm types and update our knowledge in this area.

Molecular detection of Theileria sergentii/orientalis/buffeli and Ehrlichia canis from aborted ovine and caprine products in Sardinia, Italy.

The economic impact and losses caused by abortion of small ruminants represent an important threat to livestock industry worldwide. Infectious agents are the most commonly causes of small ruminant abortion and many of which pose a serious threat to human health. The management of abortion outbreaks is essential to understand the transmission, prevention and control of the zoonotic diseases. This study aimed to increase the knowledge about the common known zoonotic pathogens causing abortion (Coxiella burnetii, Chlamydia abortus and Toxoplasma gondii) circulating in Sardinia. In addition, the occurrence of other infectious agents that, until now, had never been identified in abortion samples and which might be cocirculating during the abortion outbreaks were also considered. In this study, 125 abortion samples collected from 91 small ruminant farms were screened for the presence of Babesia/Theileria spp., Ehrlichia canis, Anaplasma spp., Chlamydia spp., C. burnetii and T. gondii by PCR analyses and sequencing. This is the first evidence on the presence of Theileria sergenti/orientalis/buffeli group and Eh. canis in 22 (22/125; 18%) and 26 (26/125; 21%) abortion products from small ruminants, respectively. Chlamydia abortus, C. burnetii and T. gondii were also detected in brain, liver, spleen and placentae at 46% (58/125), 34% (42/125) and 2% (2/125), respectively. This study highlights that pathogens with epizootic and zoonotic potential are circulating in the island and could be involved directly or in association with other pathogens as possible cause of ruminant abortion. Further studies are needed to fully assess the impact of Theileria sergenti/orientalis/buffeli group and Eh. canis on ruminant abortion and their real zoonotic risk in the island.

Welfare Assessment: Correspondence Analysis of Welfare Score and Hematological and Biochemical Profiles of Dairy Cows in Sardinia, Italy.

The need for animal welfare definition and assessment is increasing worldwide, and several studies have been conducted to help fill the knowledge gaps regarding the welfare of cattle. However, further studies are needed to provide valid synthetized measures for welfare evaluation. The aim of this study was to assess the welfare status of 16 Sardinian dairy cattle farms, based on the developed Animal Welfare and Biosecurity Evaluation checklist (AWB-EF) and the corresponding hematological, biochemical, and electrophoretic profiles of these animals. Considering the AWB-EF as gold standard, blood samples were collected from 230 Holstein breed dairy cattle, aged between 3 and 8 years, out of the periparturient period, and with no clinical signs of specific pathologies. Principal Component (PC) and correlation analyses were performed to simplify phenomena interpretation and assess positive/negative associations. Four PCs were able to explain 76% of the total variability, and six laboratory parameters were strongly associated with the AWB-EF score (Spearman's correlation coefficient ≥ 0.40, p-Value < 0.05), reflecting the real health status of the animals. Given the complexity of animal welfare as a multidimensional concept and the need to include both animal-based and non-based measures in welfare evaluation, the present work represents a sound basis for future evaluation and veterinary health planning.