Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity.

There is an increasing understanding that a reference genome representing an individual cannot capture all the gene repertoire of a species. Here, we conduct a population-scale missing sequences detection of Chinese domestic pigs using whole-genome sequencing data from 534 individuals. We identify 132.41 Mb of sequences absent in the reference assembly, including eight novel genes. In particular, the breeds spread in Chinese high-altitude regions perform significantly different frequencies of new sequences in promoters than other breeds. Furthermore, we dissect the role of non-coding variants and identify a novel sequence inserted in the 3'UTR of the FMO3 gene, which may be associated with the intramuscular fat phenotype. This novel sequence could be a candidate marker for meat quality. Our study provides a comprehensive overview of the missing sequences in Chinese domestic pigs and indicates that this dataset is a valuable resource for understanding the diversity and biology of pigs.

Impact of litter size on the hematological and iron status of gilts, sows and newborn piglets: a comparative study of domestic pigs and wild boars.

BACKGROUND: The critically low hepatic iron stores of newborn piglets are considered to be a major cause of neonatal iron deficiency in modern breeds of domestic pig (Sus domestica). The main factor believed to contribute to this phenomenon is large litter size, which has been an objective of selective breeding of pigs for decades. As consequence, iron transferred from the pregnant sow has to be distributed among a greater number of fetuses. RESULTS: Here, we investigated whether litter size influences red blood cell (RBC) indices and iron parameters in Polish Large White (PLW) piglets and gilts. Small and large litters were produced by the transfer of different numbers of embryos, derived from the same superovulated donor females, to recipient gilts. Piglets from large litters obtained following routine artificial insemination were also examined. Our results clearly demonstrated that varying the number of piglets in a litter did not affect the RBC and iron status of 1-day-old piglets, with all showing iron deficiency anemia. In contrast, gilts with small litters displayed higher RBC and iron parameters compared to mothers with large litters. A comparative analysis of the RBC status of wild boars (having less than half as many piglets per litter as domestic pigs) and PLW pigs, demonstrated higher RBC count, hemoglobin level and hematocrit value of both wild boar sows and piglets, even compared to small-litter PLW animals. CONCLUSIONS: These findings provide evidence that RBC and iron status in newborn PLW piglets are not primarily determined by litter size, and indicate the need to study the efficiency of iron transport across the placenta in domestic pig and wild boar females.

Unveiling the genetic structure of pig population in a Himalayan state Uttarakhand through microsatellite and mitochondrial DNA analyses.

This study traced the maternal lineage of the domestic swine populations using mitochondrial DNA control region markers and genetic diversity using microsatellite markers in Uttarakhand, an Indian state situated at the foothills of the world's youngest (geo-dynamically sensitive) mountain system, "the Himalayas". Analysis of 68 maternally unrelated individuals revealed 20 haplotypes. The maternal signature of the Pacific, Southeast Asian, European, and ubiquitously distributed Chinese haplotypes was present in Uttarakhand's domestic pig population. The D3 haplotype reported in wild pigs from North India was also identified in 47 domestic samples. A unique gene pool, UKD (Uttarakhand Domestic), as another lineage specific to this region has been proposed. Genotypes were analyzed, using 13 sets of microsatellite markers. The observed (Ho) and expected (He) heterozygosities were 0.83 ± 0.02 and 0.84 ± 0.01, respectively. The average polymorphic information content value of 0.83 ± 0.01 indicated the high informativeness of the marker. The overall mean FIS value for all the microsatellite markers was low (F = 0.04, P < 0.01). Seven loci deviated from Hardy-Weinberg equilibrium (HWE) at a significant level (p < 0.05). Two clusters were identified, indicating overlapping populations. These results suggested that though belonging to different maternal lineages, the traditional management practices in Uttarakhand have allowed for genetic mixing and the sharing of genetic material among pig populations. It could contribute to increased genetic diversity but might also result in the loss of distinct genetic characteristics or breed purity of the local breeds if not carefully managed.

Campylobacter magnus sp. nov., isolated from caecal contents of domestic pigs (Sus scrofa domesticus).

During the 2021 European Food Safety Authority coordinated harmonized monitoring of antimicrobial resistance in Campylobacter species in Slovenia, five Campylobacter-like strains were cultured from caeca of a total of 104 domestic pigs that could not be identified using the standard-prescribed biochemical tests or MALDI-TOF MS. The isolates were obtained using the standard ISO 10272 procedure for the isolation of thermotolerant Campylobacter with prolonged cultivation time. Small Campylobacter-like colonies were observed on mCCDA and CASA agar plates after 2-4 days of incubation; dark-field microscopy revealed relatively big spirilli-shaped bacteria exhibiting characteristic Campylobacter-like motility. The cells were 1.5-3 µm long and 0.5-0.7 µm wide, Gram-negative, oxidase-positive and catalase-positive. MALDI-TOF mass spectra were distinctive and consistent, but with low MALDI-TOF MS log scores and the closest matches being those of Campylobacter hyointestinalis and Campylobacter fetus. All five strains underwent whole-genome sequencing. Analysis of 16S rRNA gene sequences revealed that the isolates were most similar (98.3-98.4 % identity) to Campylobacter lanienae. Pairwise average nucleotide identity (ANI) values revealed that the five studied strains shared pairwise ANI of 96.2-96.5 % but were clearly distinct from the previously described Campylobacter species (ANI ≤72.8 %). The core genome-based phylogeny confirmed that the new strains form a distinct and well-supported clade within the genus Campylobacter. The conducted polyphasic taxonomic analysis confirmed that the five strains represent a novel Campylobacter species for which the name Campylobacter magnus sp. nov. is suggested, with strain 46386T (=DSM 115534T=CCUG 76865T) as the type strain.

Helicobacter colisuis sp. nov., isolated from caecal contents of domestic pigs (Sus scrofa domesticus).

Seven Helicobacter-like isolates were cultured from caecal contents of 100 domestic pigs (Sus scrofa domesticus) sampled as part of the EFSA-coordinated harmonized monitoring of antimicrobial resistance in Campylobacter sp. in 2015. The bacteria were isolated using the standard ISO 10272 procedure for the isolation of thermotolerant Campylobacter with extended incubation time and formed small, grey, moist and flat colonies with a metallic sheen (small Campylobacter-like colonies) on modified Charcoal-Cefoperazone-Deoxycholate Agar (mCCDA) and Skirow agar plates. Morphologically, the bacterial cells were spirilli-shaped and highly motile, 1-2 µm long and ≤0.5 µm wide, Gram-negative, oxidase-positive and catalase-positive. They could not be identified using the standard-prescribed biochemical tests and had uniform, unique and reproducible MALDI-TOF mass spectra that most closely matched those of Helicobacter pullorum. Three strains (11154-15T, 14348-15 and 16470-15) underwent whole-genome sequencing. Analysis of 16S rRNA gene sequences revealed a high similarity (≥99.8 % identity) to Helicobacter canadensis. Pairwise average nucleotide identity (ANI) values revealed that the three studied strains were closely related (ANI ≥98.9 %), but distinct from the previously described Helicobacter species (ANI ≤90.6 %). The core genome-based phylogeny confirmed that the new strains form a distinct clade most closely related to H. canadensis. The conducted polyphasic taxonomic analysis confirmed that the three strains represent a novel Helicobacter species for which the name Helicobacter colisuis sp. nov. is suggested, with strain 11154-15T (= DSM 113688T = CCUG 76053T) as the type strain.

Domestic pig head and neck arteries from the viewpoint of imaging methods and experimental surgery

The aim of this paper is to summarize the current knowledge of the anatomy of domestic pig head and neck arteries for the needs of experimental surgery and imaging methods in biomedical research and translational medicine. The potential of this large animal model seems to be valuable also for the xenotransplantation of certain organs. Demands for the knowledge of morphological differences between analogous human structures and particular breeds are growing also in connection with the need for more precise planning of experiments or interpretation of the results. Deepening anatomical knowledge is allowed also by the development of imaging methods. The search was performed using the keywords "domestic pig" and "arteries of the head and neck" in the MEDLINE database, PubMed interface.

Permanent intravenous access in experimental surgery ­ our experience

Introduction: Permanent intravenous access is usually required in pigs used for surgical experiments, not only to enable repeated blood sample collections. The aim of this study was to evaluate the patency and complications of vascular access ports (VAP) implanted in pigs included in different surgical experiments. Methods: VAPs were implanted via the external jugular vein in a total of 211 pigs from 7 different experiments. All observed complications were retrospectively evaluated. Results: No complications were observed in 157 animals (74.4%). Complications of the least severity were edema or seroma around the port which were observed in 12 (5.7%) and 3 (1.4%) animals, respectively. Temporary problems with aspiration of blood via the port occurred in 13 animals (6.2%). The most severe complications which prevented the use of the VAP for aspiration and application were recorded in 26 animals (12.3%). These complications included: abscess formation around the port (12 animals), skin necrosis over the port (2 animals), partial wound dehiscence (2 animals) and loss of the VAP function due to an unspecified cause (10 animals). Removal of the VAP was not needed in any of the animals and none of the animals had to be excluded from the experiment due to the complications. The VAP can also be used for safe administration of iodine contrast agent during CT examination. Conclusion: Despite the observed complications the VAP is suitable as permanent intravenous access in pigs used for surgical experiments. This method helps to minimize the stress of the animals in the postoperative period and to reduce the number of experimental animals.

African swine fever: a New Zealand perspective on epidemiological risk factors for its occurrence.

This article reviews key epidemiological and clinical features of African swine fever (ASF). We identify particular aspects of New Zealand's pig populations (commercial, non-commercial, and wild) that may affect the risk of disease entry or spread. Review of published literature is supplemented by analysis of demographic and spatial aspects of the New Zealand commercial, non-commercial, and feral pig populations to provide context around risk factors for the disease that are most relevant to New Zealand. The current Eurasian outbreak of ASF, including recent spread into Oceania, has increased the risk of an incursion of the disease into New Zealand. Large volumes of fresh pork importation (including from countries affected by ASF), large non-commercial pig populations with substantial spatial overlap with the country's commercial industry, limited monitoring of compliance with waste food feeding regulations, and lack of mandatory premises identification for non-commercial pig holdings would likely contribute to the risk of spread of ASF in the event of an incursion. Awareness amongst veterinarians of these risk factors will contribute to national biosecurity and disease preparedness efforts in New Zealand.

Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi.

Several African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

Death caused by a domestic pig attack.

The primary medico-legal investigation goal in deaths due to animal attacks is distinguishing between animal-related injuries and potential homicidal wounds. We report the case of a 49-year-old male found dead in his farm's pigsty, where a sow and her piglets were present. At the postmortem examination, numerous, severe blunt force injuries were observed on the body, with special regard to the upper extremities where massive injuries involving soft tissues, bones, and regional vessels, tendons, and nerves were present. The death resulted from severe bleeding from massive upper extremities injuries due to a domestic pig attack. Domestic pigs are usually placid but they can become aggressive if disturbed and attack humans producing severe injuries due to trampling, kicking and biting. Knowing the relevant anatomy, pattern of attack, and morphologies of wounds produced by particular animals can distinguish animal attacks from homicides, as well as attempt to identify the type of animal involved in an unwitnessed attack.

Porcine Liver Anatomy Applied to Biomedicine.

Currently, there are at least 70 pure domestic pig breeds, but only certain breeds are used in biomedical research. The domestic pig liver is suitable for preclinical research because its size, physiology, and anatomy are similar to that of the human liver; in addition, there is a high degree of genetic similarity between the two species. For planning experiments and identifying improvements in both invasive and noninvasive methods of liver disease management, the morphological similarities and dissimilarities of the pig liver to its human counterpart must be taken into consideration along with sexual dimorphism and interindividual and interspecific variability. Recent histological evaluations based on stereological methods enable precise quantitative morphological estimates and guarantee their unbiased accuracy. The results thereof are crucial for revealing and assessing histological changes and can contribute to the optimization of study designs. New trends in computed tomography data processing have also been introduced. This review article summarizes the newest trends and findings in the field of porcine liver anatomy and histology as applicable to preclinical research.

Local Tolerability and Performance Evaluation in Domestic Pigs of a Fractional Radiofrequency Device for Dermatologic Treatment.

Information on the safety of energy-based dermatological surgical devices in domestic pigs, and fractional radiofrequency (RF) devices in particular, is very limited. The aim of this study was to evaluate in a GLP-compliant study in domestic pigs the local reaction and performance of a novel fractional RF device. Five female domestic pigs were subjected to fractional RF pulses, using different energy and pulse durations and depth of penetration of the pulses. The animals were evaluated clinically and histologically at different time points (days 0, 1, 3, 7, and 14) postenergy exposure. There were no microscopic or macroscopic local adverse effects in any tested power settings, and there was time-related progressive healing, reaching complete macroscopic and microscopic healing by 7 days postapplication. As expected, there was power-related progressive increase in the incidence of ablation (destruction of skin tissue by vaporization) and coagulative necrosis of the dermis from low to high power setting. This comprehensive study, using multiple power settings (both ablative and coagulative) and several time points, will be of benefit for future studies evaluating new fractional RF devices.

The emergence of porcine epidemic diarrhoea in Croatia: molecular characterization and serology.

BACKGROUND: Porcine epidemic diarrhoea (PED) is an emergent/re-emergent viral pig disease (caused by the virus belonging to the Coronaviridae family, in specific the Alphacoronavirus genus) of global importance. Clinical presentation is characterized with acute diarrhoea, vomiting and dehydration in pigs of all ages, with a possible high mortality in suckling piglets. The disease emerged in the USA in 2013 causing heavy losses, and re-emerged in Europe in 2014, but with milder consequences. RESULTS: In the spring 2016, PED-like symptoms were reported to be seen on an agricultural holding in Eastern Croatia; laboratory workup confirmed the Croatia's first PED outbreak ever. Porcine epidemic diarrhoea virus (PEDV) strain responsible for the outbreak was of the S-INDEL genotype, much the same as other European PEDV strains. In 2017, a post-outbreak serology was carried out in three counties in Eastern Croatia, revealing seropositivity in pigs bred on four large industrial holdings (9.09%). The seroprevalence across PEDV-positive holdings was up to 82.8%. The latter holdings were unanimously managed by an enterprise that had never reported PED before. CONCLUSIONS: PED has emerged in Croatian pig population causing potentially considerable losses. The circulating strain was of the S-INDEL genotype. Serological workup proved PEDV spread to another four agricultural holdings, demonstrating the importance of not only external, but also internal biosecurity measures.

Morphological and molecular characterizations of Sarcocystis miescheriana and Sarcocystis suihominis in domestic pigs (Sus scrofa) in China.

In this study, 36.8% (28/76) of tissue samples collected from domestic pigs (Sus scrofa) contained sarcocysts, as determined by light microscopy. The organisms were identified as Sarcocystis miescheriana and Sarcocystis suihominis based on their morphological and molecular characteristics. Four genetic markers, i.e., 18S rDNA, 28S rDNA, ITS-1 region (ITS-1), and the mitochondrial COX1 gene (COX1), of the two parasites were sequenced and analyzed, and the 28S rDNA and ITS-1 of S. suihominis obtained from pigs constituted the first records of these markers in GenBank. The sequences of the four loci (18S rDNA, 28S rDNA, ITS-1, and COX1) of S. miescheriana shared high identities with those of S. miescheriana obtained from domestic and/or wild pigs in GenBank, with similarities of 99.6%, 99.6%, 95.9%, and 95.4%, respectively. The 18S rDNA sequences of S. suihominis exhibited 99.4% identity with those of S. suihominis from domestic and wild pigs. The comparison of the newly obtained sequences of the four genetic markers between the two parasites revealed that the interspecific similarities of 18S rDNA, 28S rDNA, ITS-1, and COX1 were 97.7%, 96.6%, 80.3%, and 81.2%, respectively. Therefore, the two species could be better discriminated with ITS-1 and mitochondrial COX1 compared with 18S rDNA or 28S rDNA. The phylogenetic analysis using 28S rDNA indicated that the two Sarcocystis species in domestic pigs had a close relationship.

Identification of Wild Boar-Habitat Epidemiologic Cycle in African Swine Fever Epizootic.

The African swine fever epizootic in central and eastern European Union member states has a newly identified component involving virus transmission by wild boar and virus survival in the environment. Insights led to an update of the 3 accepted African swine fever transmission models to include a fourth cycle: wild boar-habitat.

Outbreaks of Neuroinvasive Astrovirus Associated with Encephalomyelitis, Weakness, and Paralysis among Weaned Pigs, Hungary.

A large, highly prolific swine farm in Hungary had a 2-year history of neurologic disease among newly weaned (25- to 35-day-old) pigs, with clinical signs of posterior paraplegia and a high mortality rate. Affected pigs that were necropsied had encephalomyelitis and neural necrosis. Porcine astrovirus type 3 was identified by reverse transcription PCR and in situ hybridization in brain and spinal cord samples in 6 animals from this farm. Among tissues tested by quantitative RT-PCR, the highest viral loads were detected in brain stem and spinal cord. Similar porcine astrovirus type 3 was also detected in archived brain and spinal cord samples from another 2 geographically distant farms. Viral RNA was predominantly restricted to neurons, particularly in the brain stem, cerebellum (Purkinje cells), and cervical spinal cord. Astrovirus was generally undetectable in feces but present in respiratory samples, indicating a possible respiratory infection. Astrovirus could cause common, neuroinvasive epidemic disease.

Domestic Pig Unlikely Reservoir for MERS-CoV.

We tested the suitability of the domestic pig as a model for Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Inoculation did not cause disease, but a low level of virus replication, shedding, and seroconversion were observed. Pigs do not recapitulate human MERS-CoV and are unlikely to constitute a reservoir in nature.

Honest signaling in domestic piglets (Sus scrofa domesticus): vocal allometry and the information content of grunt calls.

The information conveyed in acoustic signals is a central topic in mammal vocal communication research. Body size is one form of information that can be encoded in calls. Acoustic allometry aims to identify the specific acoustic correlates of body size within the vocalizations of a given species, and formants are often a useful acoustic cue in this context. We conducted a longitudinal investigation of acoustic allometry in domestic piglets (Sus scrofa domesticus), asking whether formants of grunt vocalizations provide information concerning the caller's body size over time. On four occasions, we recorded grunts from 20 kunekune piglets, measured their vocal tract length by means of radiographs (X-rays) and weighed them. Controlling for effects of age and sex, we found that body weight strongly predicts vocal tract length, which in turn determines formant frequencies. We conclude that grunt formant frequencies could allow domestic pigs to assess a signaler's body size as it grows. Further research using playback experiments is needed to determine the perceptual role of formants in domestic pig communication.

Identification and genetic characterization of two porcine astroviruses from domestic piglets in China.

Porcine astrovirus are divided into five genotypes. In this study, we identified two porcine astroviruses (AstV-LL-1 and AstV-LL-2) by using sequence-independent single-primer amplification (SISPA) on faecal specimens of healthy domestic piglets younger than 15 days. The detection rate for both was 2.82% (14/497). AstV-LLs were then sequenced and characterised. Phylogenetic analysis revealed that they have the characteristics of porcine astrovirus (PastV) 2 and 5 and have some unique genetic features. Our findings show that the two astroviruses are novel lineages of PAstV2 and 5. The findings may be helpful in evaluating the ecology and evolution of astroviruses in pigs.

Brucella suis infection in domestic pigs in Sardinia (Italy).

During a 4-year (2007-2010) survey, the presence of Brucella suis infection in domestic pigs in Sardinia was investigated. Serum samples were collected from breeding pigs located on 108 commercial farms with documented reproductive problems and analysed using the Rose Bengal (RBT) and complement fixation (CFT) tests for screening and confirmation of Brucella, respectively. Of the 1251 serum samples analysed by RBT, 406 sera, originating from 36 farms, were positive for B. suis. CFT was positive in 292/748 sera analysed, confirming positivity in all 36 pig herds. Pigs with international complement fixation test units per ml (ICFTU/ml) values ⩾160 were slaughtered, and their organs collected for bacteriological examination and testing by polymerase chain reaction (PCR). Brucella spp. strains were isolated in culture from 13/502 organs analysed, and subsequently identified as B. suis biovar 2. PCR detected positivity to Brucella spp. in 19/285 organs analysed. These results confirm the presence and emergence of B. suis infection in domestic pigs in Sardinia.