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Background Currently, eight species in four genera of parvovirus have been described that infect swine. These include ungulate protoparvovirus 1 (classical porcine parvovirus, PPV), ungulate tetraparvovirus 2 (PPV3), ungulate tetraparvovirus 3 (which includes PPV2, porcine hokovirus, porcine partetravirus and porcine PARV4), ungulate copiparvovirus 2 (which includes PPV4 and PPV5), ungulate bocaparvovirus 2 (which includes porcine bocavirus 1, 2 and 6), ungulate bocaparvovirus 3 (porcine bocavirus 5), ungulate bocaparvovirus 4 (porcine bocavirus 7) and ungulate bocaparvovirus 5 (porcine bocavirus 3, 4–1 and 4–2). PPV6, the most recently described porcine parvovirus, was first identified in China in late 2014 in aborted pig fetuses. Prevalence of PPV6 in China was found to be similar in finishing age pigs from farms with and without evidence of swine reproductive failure. Methods Porcine parvovirus 6 (PPV6) was detected by sequence-independent single primer amplification (SISPA) and confirmed by overlapping and real-time PCR in the serum of porcine reproductive and respiratory virus (PRRSv) positive samples. Results Seven nearly complete genomes of PPV6 were identified in PRRSv genotype 2 positive serum samples submitted to state veterinary diagnostic laboratories in 2014. Further testing using overlapping and real-time PCR determined PPV6 to be present in 13.2 % of the serums tested. Additionally, PPV6 was present in samples from all of the geographic locations sampled encompassing nine states in the United States and one state in Mexico. The presence of PPV6 in serum indicates that the PPV6 infection is disseminated and not localized to a specific tissue type. Alignments of the near full length genomes, NS1, and capsid genes identified one of the five PPV6 isolates from China (98.6–99.5 % identity with the North American strains) to be the North American strains nearest relative. Conclusions These results are the first to report the presence of PPV6 in North America and demonstrate that the virus is found in multiple geographic areas in the United States and in Mexico. The overall prevalence of PPV6 in PRRSv viremic animals is relatively low. Further, all of the PPV6 genomes found in North America are most closely related to a PPV6 strain first identified in 2014 in healthy pigs from the Tianjin province of China.

Ungulate protoparvovirus 1, also known as porcine parvovirus 1 (PPV1), is considered to be one of the major causes of reproductive failure in pig breeding herds. Other parvoviruses have also been identified in pigs, including ungulate tetraparvovirus 3, or PPV2, ungulate tetraparvovirus 2, or PPV3, and ungulate copiparvovirus 2, or PPV4, but their significance for pigs is unknown. In the present study, the prevalence of PPV1-4 was investigated using a total of 231 lung and serum samples collected from slaughterhouses in 13 provinces throughout Vietnam. The overall prevalence was 54.5% (126/231) for PPV1, 28.0% (65/231) for PPV2, 17.7% (41/231) for PPV3, and 7.8% (18/231) for PPV4. While PPV1 and PPV2 were found in 11 provinces, PPV4 was detected in only three provinces. Co-circulation of PPV1, PPV2 and PPV3 was frequently observed, with PPV1/PPV2 coinfection predominating, with 20.8% (48/231). All four PPVs were detected together in only one sample from Thua Thien Hue. Three nearly complete PPV4 genome sequences of 5,453 nt were determined and deposited in the GenBank database. Alignment and comparison of the three genome sequences showed 99.5-99.6% nucleotide sequence identity, and the deduced amino acid sequences of open reading frames 1-3 were 99.6-99.9% identical to each other, 98.9-99.3% identical to those of other Vietnamese strains and 99.4-99.7% identical to those of Chinese strains). Phylogenetic analysis further confirmed a close relationship between Vietnamese and Chinese PPV4 strains. These results are the first to report the prevalence of PPV1, PPV2, PPV3, and PPV4 and nearly complete genomic sequences of PPV4 in pigs from slaughterhouses in Vietnam.

Modern pig farming is characterised by the emergence of several syndromes whose aetiology is unclear or has a multifactorial origin, including periweaning failure-to-thrive syndrome (PFTS). In fact, its specific aetiology remains elusive, although several causes have been investigated over time. The present study aimed to investigate the potential role of viral agents in PFTS-affected and healthy animals by evaluating the virome composition of different organs using a metagenomic approach. This analysis allowed demonstrating a higher abundance of Porcine parvovirus 6 (PPV6) in healthy subjects while Ungulate bocaparvovirus 2 (BoPV2), Ungulate protoparvovirus 1 (PPV) and Porcine circovirus 3 (PCV-3) were increased in pigs with PFTS. No differential abundance of RNA viruses was found between PFTS-affected and control pigs. Remarkably, this is the first molecular characterisation of PPV6 and BoPV2 in Spain and one of the few all around the world, supporting their apparent widespread circulation. Interestingly, PCV-3 has been recently identified in several clinical-pathological conditions as well as in healthy pigs, while BoPV2 pathogenic potential is unknown. Although obtained results must be taken as preliminary, they open the door for further studies on the potential role of these viruses or their combination as predisposing factor/s for PFTS occurrence.

The red deer is an ungulate and large game species. The contamination of the ecosystems by metal(loid)s may lead to the exposure of animals (as well as humans) through water and food resources. The direct contact of hunters and wild animal meat consumers with deer carcasses may be a potential contaminant source. This study aimed to determine the metal(loid)s’ concentrations in the liver and kidney of red deer from two regions of Portugal (Idanha-a-Nova and Lousã), and to relate these with histopathologic lesions. Thirteen young male deer were submitted to metal(loid) determination (As, Cd, Co, Cr, Cu, Pb, and Zn) by inductively coupled plasma mass spectrophotometry (ICP-MS) and histopathology examination. Renal Cd (8.072 ± 5.766 mg/kg dw) and hepatic Pb (3.824 ± 6.098 mg/kg dw) mean values were high, considering the maximum values for consumption established by the European Commission. The hepatic mean value of Cu was significantly higher in Idanha-a-Nova (150.059 ± 33.321 mg/kg dw), and it is at the Cu toxicity limit considered for ruminants (150 mg/kg). The pollution induced by Panasqueira mines (Castelo Branco) may be a possible explanation for some of the findings, especially the higher values of hepatic Cu and Pb found in Idanha-a-Nova deer. These results have high importance under a One Health perspective, since they have implications in public health, and pose at risk the imbalance of animal populations and ecosystems.

Background Atypical porcine pestivirus (APPV) is a novel, highly variable porcine pestivirus. Previous reports have suggested that the virus is associated with congenital tremor (CT) type A-II in piglets, and little information is available about the correlation between the virus and sow abortion, or on coinfection with other viruses. In China, reported APPV strains were mainly isolated from South China and Central China, and data about the APPV genome from northern China are relatively scarce. Methods Eleven umbilical cords, one placenta, and one aborted piglet, were collected from aborted sows of the same farm in Shandong Province of northern China. Nucleic acids were extracted from the above samples, and subsequently pooled for viral metagenomics sequencing and bioinformatics analysis. The viral coexistence status and complete genome characteristics of APPV in Shandong Province were determined. Results In abortion cases, APPV was present with Getah virus, porcine picobirnavirus, porcine kobuvirus, porcine sapovirus, Po-Circo-like virus, porcine serum-associated circular virus, porcine bocavirus 1, porcine parvovirus 1, porcine parvovirus 3 and porcine circovirus 3, etc. The first complete genome sequence(11,556 nt) of APPV in Shandong Province of northern China, was obtained using viral metagenomics and designated APPV-SDHY-2022. Comparison with Chinese reference strains revealed that the polyprotein of APPV-SDHY-2022 shared 82.6-84.2%, 93.2-93.6%, and 80.7-85% nucleotide identity and 91.4-92.4%, 96.4-97.7%, and 90.6-92.2% amino acid identity with those of the Clade I, Clade II and Clade III strains, respectively. Phylogenetic analysis based on the complete polyprotein CDS and NS5A sequences concluded that APPV-SDHY-2022 belongs to Clade II. Analysis of the NS5A nucleotide sequences revealed homology of greater than 94.6% for the same isoform, 84.7-94.5% for different isoforms of the same clade and 76.8-81.1% for different clades. Therefore, Clade II was further divided into three subclades, and APPV-SDHY-2022 belonged to subclade 2.3. Members of Clade II have 20 unique amino acids in individual proteins, distinguishing them from Clade I and Clade III members. The E2 protein showed the greatest diversity of putative N-glycosylation sites with 9 patterns, and APPV-SDHY-2022 along with other Chinese APPV strains shared the conserved B-cell conformational epitope residues 39E, 70R, 173R, 190K and 191N of the E2 protein. Conclusions We reported viral coexistence and the first complete genome sequence of APPV from abortion cases and from Shandong Province. The new APPV isolate belongs to an independent branch of Clade II. Our results increase the molecular and epidemiological understanding of APPV in China.

Migratory ungulates are thought to be declining globally because their dependence on large landscapes renders them highly vulnerable to environmental change. Yet recent studies reveal that many ungulate species can adjust their migration propensity in response to changing environmental conditions to potentially improve population persistence. In addition to the question of whether to migrate, decisions of where and when to migrate appear equally fundamental to individual migration tactics, but these three dimensions of plasticity have rarely been explored together. Here, we expand the concept of migratory plasticity beyond individual switches in migration propensity to also include spatial and temporal adjustments to migration patterns. We develop a novel typological framework that delineates every potential change type within the three dimensions, then use this framework to guide a literature review. We discuss broad patterns in migratory plasticity, potential drivers of migration change, and research gaps in the current understanding of this trait. Our result reveals 127 migration change events in direct response to natural and human-induced environmental changes across 27 ungulate species. Species that appeared in multiple studies showed multiple types of change, with some exhibiting the full spectrum of migratory plasticity. This result highlights that multidimensional migratory plasticity is pervasive in ungulates, even as the manifestation of plasticity varies case by case. However, studies thus far have rarely been able to determine the fitness outcomes of different types of migration change, likely due to the scarcity of long-term individual-based demographic monitoring as well as measurements encompassing a full behavioral continuum and environmental gradient for any given species. Recognizing and documenting the full spectrum of migratory plasticity marks the first step for the field of migration ecology to employ quantitative methods, such as reaction norms, to predict migration change along environmental gradients. Closer monitoring for changes in migratory propensity, routes, and timing may improve the efficacy of conservation strategies and management actions in a rapidly changing world.

Illuminating the ecological and evolutionary dynamics of parasites is one of the most pressing issues facing modern science, and is critical for basic science, the global economy, and human health. Extremely important to this effort are data on the disease-causing organisms of wild animal hosts (including viruses, bacteria, protozoa, helminths, arthropods, and fungi). Here we present an updated version of the Global Mammal Parasite Database, a database of the parasites of wild ungulates (artiodactyls and perissodactyls), carnivores, and primates, and make it available for download as complete flat files. The updated database has more than 24,000 entries in the main data file alone, representing data from over 2700 literature sources. We include data on sampling method and sample sizes when reported, as well as both \"reported\" and \"corrected\" (i.e., standardized) binomials for each host and parasite species. Also included are current higher taxonomies and data on transmission modes used by the majority of species of parasites in the database. In the associated metadata we describe the methods used to identify sources and extract data from the primary literature, how entries were checked for errors, methods used to georeference entries, and how host and parasite taxonomies were standardized across the database. We also provide definitions of the data fields in each of the four files that users can download.

More than a quarter of earth's land surface is used for grazing domestic livestock. Livestock grazing is generally assumed to negatively affect wildlife, however, a number of studies have found positive impacts as well. We conducted an evidence-based review of the existing literature using a series of livestock- and wildlife-related search words to systematically query Google Scholar and Web of Science. A total of 807 sources were included in the final list, including 646 primary sources which reported original data. The majority of studies were conducted in North America (338) or Europe (123), with many fewer from Africa (57), Australia (54), Central/South America (43), or Asia (31). Most studies examined birds (330) and mammals (262), with fewer including reptiles (91) or amphibians (58). We extracted further information from studies that included mammals on positive, negative, and neutral effects of livestock grazing on mammals. We found that livestock change vegetation structure and cover in ways important to small mammals, while ungulates may be affected more by interference competition and changes in forage quantity and quality. Community-level total abundance of small mammals typically declines with grazing. Species richness of small mammals either declines or stays the same, as many studies found a change in species composition from ungrazed to grazed sites while the number of species remained similar. Individual species responses of small mammals vary. Voles, harvest mice, cotton rats, and shrews show consistently negative responses to grazing while deer mice, kangaroo rats, ground squirrels, and lagomorphs show positive or variable responses. In general, species adapted to open habitats are often positively affected by grazing, while species needing denser cover are negatively affected. Studies of wild ungulates are more variable in methodology and quality than those for small mammals. We found more negative (n = 86) than positive (n = 34) ungulate responses overall, however, most studies have been on browsers and mixed feeders, namely deer and elk, and there is little available data for other groups. Although data is limited, several of the grazing species in Africa may show a trend toward positive responses, suggesting possible facilitation. For a number of species, responses varied by season. We find a strong need for additional research on ungulates of varying diets and body sizes, especially in the developing world, and across longer time scales to examine possible tradeoffs between competition and facilitation from livestock.

Ungulates have become abundant in many temperate forests, shifting tree species composition by browsing and altering soil physical conditions by trampling. Whether these effects cascade down to other trophic levels and ecosystem processes is poorly understood. Here, we assess the paths through which ungulates have cascading effects on other trophic levels (regeneration, litter, invertebrates, rodents and organic matter decomposition). We compared ungulate effects by comparing 15 response variables related to different trophic levels between paired fenced and unfenced plots in twelve temperate forest sites across the Netherlands, and used pathway analysis model to identify the (in)direct pathways through which ungulates have influenced these variables. We found that plots with ungulates (that is, unfenced) compared to plots without (that is, fenced) had lower litter depth, sapling diversity, sapling density, rodent activity, macro-invertebrate biomass, decomposition rate of tea bags, pine and birch litter and higher soil compaction. These findings were used in a path analysis to establish potential causal relationships, which showed that ungulate presence: decreased sapling density, which indirectly decreased rodent activity; decreased litter depth, which indirectly reduced invertebrate diversity; increased soil compaction, which also decreased invertebrate diversity. Soil pH decreased invertebrate biomass, which also increased nitrogen mineralization. Yet, we did not find cascading effects of ungulates on decomposition rates. Importantly, an increase in ungulate abundance strengthens the cascading effects in this system. Our results suggest that ungulates can trigger cascading effects on lower trophic levels, yet decomposition and mineralization rates are resilient to ungulate browsing and trampling. Therefore, temperate forests conservation could benefit by limiting ungulate abundance.

Migratory animals are predicted to enhance lifetime fitness by obtaining higher quality forage and/or reducing predation risk compared to non‐migratory conspecifics. Despite evidence for behavioural flexibility in other taxa, previous research on large mammals has often assumed that migratory behaviour is a fixed behavioural trait. Migratory behaviour may be plastic for many species, although few studies have tested for individual‐level flexibility using long‐term monitoring of marked individuals, especially in large mammals such as ungulates. We tested variability in individual migratory behaviour using a 10‐year telemetry data set of 223 adult female elk (Cervus elaphus) in the partially migratory Ya Ha Tinda population in Alberta, Canada. We used net squared displacement (NSD) to classify migratory strategy for each individual elk‐year. Individuals switched between migrant and resident strategies at a mean rate of 15% per year, and migrants were more likely to switch than residents. We then tested how extrinsic (climate, elk/wolf abundance) and intrinsic (age) factors affected the probability of migrating, and, secondly, the decision to switch between migratory strategies. Over 630 individual elk‐years, the probability of an individual elk migrating increased following a severe winter, in years of higher wolf abundance, and with increasing age. At an individual elk level, we observed 148 switching events of 430 possible transitions in elk monitored at least 2 years. We found switching was density‐dependent, where migrants switched to a resident strategy at low elk abundance, but residents switched more to a migrant strategy at high elk abundance. Precipitation during the previous summer had a weak carryover effect, with migrants switching slightly more following wetter summers, whereas residents showed the opposite pattern. Older migrant elk rarely switched, whereas resident elk switched more frequently to migrate at older ages. Our results show migratory behaviour in ungulates is an individually variable trait that can respond to intrinsic, environmental and density‐dependent forces. Different strategies had opposing responses to density‐dependent and intrinsic drivers, providing a stabilizing mechanism for the maintenance of partial migration and demographic fitness in this population.