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The infectious bursal disease virus (IBDV) is a significant pathogen affecting the poultry industry worldwide. Its epidemiological history has been marked by the emergence of strains with different antigenic, pathogenic, and genetic features, some of which have shown notable spread potential. The A2dB1b genotype, also known as novel variant, has become widespread and gained increased relevance in IBDV epidemiology. This genotype was described in China in the 2010s and rapidly spread in Asia and Africa. The present study describes the circulation of the A2dB1b genotype in Argentina. Applying a next-generation sequencing approach, we obtained the complete coding sequence of 18 Argentine viruses. The high level of genomic homogeneity observed amongst these viruses, their monophyletic clustering in both partial and complete segments A and B derived phylogenies, and their close relatedness to some Chinese strains suggest that a unique transcontinental spread event from China to Argentina occurred recently. The apparent success of the A2dB1b genotype spreading throughout Asia, Africa, and South America may partially be due to specific amino acid characteristics. Novel residues in the hypervariable region of VP2 may help A2dB1b IBDVs evade the protection elicited by the applied commercial vaccines. Our findings underscore the importance of continuous characterization of field samples and evaluation of the control measures currently applied to fight against this specific IBDV genotype. [ABSTRACT FROM AUTHOR]

The Equid alphaherpesvirus type 1 (EHV-1) infection can have devastating economic consequences in the horse industry due to large-scale outbreaks of abortions, perinatal foal mortality, and myeloencephalopathy. The present study analyzed the genome of two isolates obtained from aborted fetuses in Argentina, E/745/99 and E/1297/07. The E745/99 genome shares 98.2% sequence identity with Ab4, a reference EHV-1 strain. The E/1297/07 genome shares 99.8% identity with NY03, a recombinant strain containing part of ORF64 and part of the intergenic region from Equid alphaherpesvirus-4 (EHV-4). The E/1297/07 genome has the same breakpoints as other United States and Japanese recombinants, including NY03. The recombinant regions have varying numbers of tandem repeat sequences and different minor parental sequences (EHV-4), suggesting distinct origins of the recombinant events. These are the first complete genomes of EHV-1 from Argentina and South America available in the Databases. [ABSTRACT FROM AUTHOR]

Bovine torovirus (BToV) is an enteric pathogen that may cause diarrhea in calves and adult cattle, which could result in economic losses due to weight loss and decreased milk production. This study aimed to report the presence, the genetic characterization and the evolution of BToV in calves in Uruguay. BToV was detected in 7.9% (22/278) of fecal samples, being identified in dairy (9.2%, 22/239) but not beef (0.0%, 0/39) calves. BToV was detected in both diarrheic (14%, 6/43) and non-diarrheic (13.2%, 5/38) dairy calves. In addition, BToV was detected in the intestinal contents of 14.9% (7/47) of naturally deceased dairy calves. A complete genome (28,446 nucleotides) was obtained, which was the second outside Asia and the first in Latin America. In addition, partial S gene sequences were obtained to perform evolutionary analyses. Nucleotide and amino acid substitutions within and between outbreaks/farms were observed, alerting the continuous evolution of the virus. Through Bayesian analysis using BEAST, a recent origin (mid-60s) of BToV, possibly in Asia, was estimated, with two introductions into Uruguay from Asia and Europe in 2004 and 2013, respectively. The estimated evolutionary rate was 1.80 × 10−3 substitutions/site/year. Our findings emphasize the importance of continued surveillance and genetic characterization for the effective management and understanding of BToV's global epidemiology and evolution. [ABSTRACT FROM AUTHOR]

This pioneering study in Spain in this specific area of knowledge, social work and social services, is framed around the incorporation of Virtual Reality (VR) in the social work teaching-learning process using 360º videos during the COVID-19 pandemic. Owing to the impossibility of face-to-face interaction, in order to put theory into practice, a VR simulation application—the Innovation Social Work App (iSWAPP) – was developed (intellectual property registration number 04/2021/491). In order to study the factors that determine the predisposition of social work students to use VR as a complementary pedagogical tool in the theory-practice learning process to acquire professional skills, a quantitative analysis was performed using the Technology Acceptance Model (TAM). The study was performed in May 2021 during the COVID-19 pandemic with a sample comprising 42 social work undergraduates at the University of Cádiz. The most significant results were the opportunities and potential of VR in the teaching-learning process, especially in teaching practice. The conclusions of the study show that 360° VR enables progress to be made in response to the structural need to build positive bidirectional synergies between theory and practice in social work in order to improve the quality of professional intervention. [ABSTRACT FROM AUTHOR]

The highly pathogenic avian influenza viruses of clade 2.3.4.4b have caused unprecedented deaths in South American wild birds, poultry, and marine mammals. In September 2023, pinnipeds and seabirds appeared dead on the Uruguayan Atlantic coast. Sixteen influenza virus strains were characterized by real-time reverse transcription PCR and genome sequencing in samples from sea lions (Otaria flavescens), fur seals (Arctocephalus australis), and terns (Sterna hirundinacea). Phylogenetic and ancestral reconstruction analysis showed that these strains have pinnipeds most likely as the ancestral host, representing a recent introduction of clade 2.3.4.4b in Uruguay. The Uruguayan and closely related strains from Peru (sea lions) and Chile (sea lions and a human case) carry mammalian adaptative residues 591K and 701N in the viral polymerase basic protein 2 (PB2). Our findings suggest that clade 2.3.4.4b strains in South America may have spread from mammals to mammals and seabirds, revealing a new transmission route. [ABSTRACT FROM AUTHOR]

Hepatitis E Virus (HEV) infection is an emergent zoonotic disease of increasing concern in developed regions. HEV genotype 3 (HEV-3) is mainly transmitted through consumption of contaminated food in high-income countries and is classified into at least 13 subtypes (3a–3n), based on p-distance values from complete genomes. In Latin America, HEV epidemiology studies are very scant. Our group has previously detected HEV3 in clinical cases, swine, wild boars, captive white-collared peccaries, and spotted deer from Uruguay. Herein, we aimed to provide novel insights and an updated overview of the molecular epidemiology of zoonotic HEV in Uruguay, including data from wastewater-based surveillance studies. A thorough analysis of HEV whole genomes and partial ORF2 sequences from Uruguayan human and domestic pig strains showed that they formed a separate monophyletic cluster with high nucleotide identity and exhibited p-distance values over the established cut-off (0.093) compared with reference subtypes' sequences. Furthermore, we found an overall prevalence of 10.87% (10/92) in wastewater, where two samples revealed a close relationship with humans, and animal reservoirs/hosts isolates from Uruguay. In conclusion, a single, new HEV-3 subtype currently circulates in different epidemiological settings in Uruguay, and we propose its designation as 3o along with its reference sequence. [ABSTRACT FROM AUTHOR]

Background: Avian influenza viruses (genus Alphainfluenzavirus, family Orthomyxoviridae) infect avian and mammal hosts. In 2022, the high pathogenicity avian influenza virus (H5N1) spread to South America, resulting in the loss of thousands of wild birds, including endangered species, and severely impacting the global poultry industry. Objectives: We analyzed the complete genomes of influenza viruses obtained from wild birds and backyard poultry in Uruguay between February and May 2023. Methods: Twelve complete genomes were obtained in 2023 from cloacal swabs using Illumina sequencing. Genomes were phylogenetically analyzed with regional and global strains. Findings: The identified strains have multiple basic amino acids at the hemagglutinin cleavage sites, which is typical for highly pathogenic strains. The Uruguayan viruses belonged to hemagglutinin clade 2.3.4.4b of the H5N1 subtype. A reassortment in North America has resulted in some segments of South American strains being of Eurasian or North American origins. The Uruguayan viruses shared a common ancestor with South American strains from Argentina and Chile. The influenza viruses displayed a spatiotemporal divergence pattern rather than being host-specific. Main Conclusions: The arrival of the 2.3.4.4b clade in Uruguay may have been mediated by birds that acquired the virus from Argentine and Chilean waterfowl migrating in the Pacific Flyway. [ABSTRACT FROM AUTHOR]

The avian infectious bronchitis virus (IBV) is a coronavirus that mutates frequently, leading to a contagious and acute disease that results in economic losses to the global poultry industry. Due to its genetic and serological diversity, IBV poses a challenge in preventing and controlling the pathogen. The full-length S1 sequence analysis identifies seven main genotypes (GI–GVII) comprising 35 viral lineages. In addition to the previously described lineage, a new GI lineage (GI-30) and two lineages from novel genotypes (GVIII-1 and GIX-1) have been described in Mexico. To prevent the spread of IBV outbreaks in a specific geographic location and select the suitable vaccine, it is helpful to genetically identify the circulating IBV types. Moreover, sequencing genomes can provide essential insights into virus evolution and significantly enhance our understanding of IBV variability. However, only genomes of previously described lineages (GI-1, GI-9, GI-13, and GI-17) have been reported for Mexican strains. Here, we sequenced new genomes from Mexican lineages, including the indigenous GI-30, GVIII-1, and GIX-1 lineages. Comparative genomics reveals that Mexico has relatively homogenous lineages (i.e., GI-13), some with greater variability (i.e., GI-1 and GI-9), and others extremely divergent (GI-30, GVIII-1, and GIX-1). The circulating lineages and intra-lineage variability support the unique diversity and dynamic of Mexican IBV. [ABSTRACT FROM AUTHOR]

A methodological approach based on reverse transcription (RT)-multiplex PCR followed by next-generation sequencing (NGS) was implemented to identify multiple respiratory RNA viruses simultaneously. A convenience sampling from respiratory surveillance and SARS-CoV-2 diagnosis in 2020 and 2021 in Montevideo, Uruguay, was analyzed. The results revealed the cocirculation of SARS-CoV-2 with human rhinovirus (hRV) A, B and C, human respiratory syncytial virus (hRSV) B, influenza A virus, and metapneumovirus B1. SARS-CoV-2 coinfections with hRV or hRSV B and influenza A virus coinfections with hRV C were identified in adults and/or children. This methodology combines the benefits of multiplex genomic amplification with the sensitivity and information provided by NGS. An advantage is that additional viral targets can be incorporated, making it a helpful tool to investigate the cocirculation and coinfections of respiratory viruses in pandemic and post-pandemic contexts. [ABSTRACT FROM AUTHOR]

The gammacoronavirus avian infectious bronchitis virus (IBV) is a highly contagious respiratory pathogen of primary economic importance to the global poultry industry. Two IBV lineages (GI-11 and GI-16) have been widely circulating for decades in South America. GI-11 is endemic to South America, and the GI-16 is globally distributed. We obtained full-length IBV genomes from Argentine and Uruguayan farms using Illumina sequencing. Genomes of the GI-11 and GI-16 lineages from Argentina and Uruguay differ in part of the spike coding region. The remaining genome regions are similar to the Chinese and Italian strains of the GI-16 lineage that emerged in Asia or Europe in the 1970s. Our findings support that the indigenous GI-11 strains recombine extensively with the invasive GI-16 strains. During the recombination process, GI-11 acquired most of the sequences of the GI-16, retaining the original S1 sequence. GI-11 strains with recombinant genomes are circulating forms that underwent further local evolution. The current IBV scenario in South America includes the GI-16 lineage, recombinant GI-11 strains sharing high similarity with GI-16 outside S1, and Brazilian GI-11 strains with a divergent genomic background. There is also sporadic recombinant in the GI-11 and GI-16 lineages among vaccine and field strains. Our findings exemplified the ability of IBV to generate emergent lineage by using the S gene in different genomic backgrounds. This unique example of recombinational microevolution underscores the genomic plasticity of IBV in South America. [ABSTRACT FROM AUTHOR]

Deletions frequently occur in the six accessory genes of SARS-CoV-2, but most genomes with deletions are sporadic and have limited spreading capability. Here, we analyze deletions in the ORF7a of the N.7 lineage, a unique Uruguayan clade from the Brazilian B.1.1.33 lineage. Thirteen samples collected during the early SARS-CoV-2 wave in Uruguay had deletions in the ORF7a. Complete genomes were obtained by Illumina next-generation sequencing, and deletions were confirmed by Sanger sequencing and capillary electrophoresis. The N.7 lineage includes several individuals with a 12-nucleotide deletion that removes four amino acids of the ORF7a. Notably, four individuals underwent an additional 68-nucleotide novel deletion that locates 44 nucleotides downstream in the terminal region of the same ORF7a. The simultaneous occurrence of the 12 and 68-nucleotide deletions fuses the ORF7a and ORF7b, two contiguous accessory genes that encode transmembrane proteins with immune-modulation activity. The fused ORF retains the signal peptide and the complete Ig-like fold of the 7a protein and the transmembrane domain of the 7b protein, suggesting that the fused protein plays similar functions to original proteins in a single format. Our findings evidence the remarkable dynamics of SARS-CoV-2 and the possibility that single and consecutive deletions occur in accessory genes and promote changes in the genomic organization that help the virus explore genetic variations and select for new, higher fit changes. [ABSTRACT FROM AUTHOR]

The analysis of genetic diversity in SARS‐CoV‐2 is the focus of several studies, providing insights into how the virus emerged and evolves. Most common changes in SARS‐CoV‐2 are single or point nucleotide substitutions; meanwhile, insertions and deletions (indels) have been identified as a less frequent source of viral genetic variability. Here, we report the emergence of a 12‐nucleotide deletion in ORF7a, resulting in a 4‐amino acid in‐frame deletion. The Δ12 variant was identified in viruses from patients of a single outbreak and represents the first report of this deletion in South American isolates. Phylogenetic analysis revealed that Δ12 strains belong to the lineage B.1.1 and clustered separated from the remaining Uruguayan strains. The ∆12 variant was detected in 14 patients of this outbreak by NGS sequencing and/or two rapid and economic methodologies: Sanger amplicon sequencing and capillary electrophoresis. The presence of strong molecular markers as the deletion described here are useful for tracking outbreaks and reveal a significant aspect of the SARS‐CoV‐2 evolution on the robustness of the virus to keep its functionality regardless loss of genetic material. [ABSTRACT FROM AUTHOR]

Chicken anaemia virus (CAV) is a widespread pathogen that causes immunosuppression in chickens. The virus-induced immunosuppression often results in secondary infections and a sub-optimal response to vaccinations, leading to high mortality rates and significant economic losses in the poultry industry. The small circular ssDNA genome (2.3 kb) has three partially overlapping genes: vp1, vp2 and vp3. VP1 capsid protein is highly variable and contains the neutralizing epitopes. Here, we analysed CAV strains from Uruguay using the full-length vp1 gene and performed a global comparative analysis to provide new evidence about the origin, dispersion and genetic variability of the virus. The phylogenetic analysis classified CAV in three or four major clades. Two clades (II and III) grouped most of the strains circulating worldwide including the Uruguayan strains. The phylodynamic analyses indicated that CAV emerged in the early 1900s and diverged to originate clade II and III. This early period of viral emergence was characterised by local diversification promoted by the extremely high substitution rate inferred for the virus (3.8 × 10−4 substitutions/site/year). Later, the virus underwent a global spreading by intra- and inter-continental migrations that correlates with a significant rise in the effective population size. In South America, CAV was introduced in three different migratory events and spread across the continent. Our findings suggest that the current CAV distribution is the consequence of its continuous expansion capability that homogenizes the populations and prevents the detection of clear temporal and geographic patterns of evolution in most strains. RESEARCH HIGHLIGHTS Current strains of chicken anaemia virus emerged in Asia in the early 1900s. Chicken anaemia virus has a high substitution rate. The phylogenetic analysis classified chicken anaemia virus in four major clades. Evolution in South America was characterized by long migration and local spreading. [ABSTRACT FROM AUTHOR]

Background: Ichthyosis is a heterogeneous group of diseases caused by genetic disorders related to skin formation. They are characterized by generalized dry skin, scaling, hyperkeratosis and frequently associated with erythroderma. Among its different types, harlequin ichthyosis (HI) stands out due to its severity. HI is caused by mutations in the ABCA12 gene, which encodes essential proteins in epidermal lipid transport, and it helps maintain the homeostasis of the stratum corneum of the epidermis. However, due to the wide spectrum of genetic alterations that can cause ichthyosis, holistic medical care, and genetic studies are required to improve the diagnosis and outcomes of these diseases. Case presentation: Here, we presented the case of a 19 years old male patient who was a premature infant and exhibited clinical features consistent with HI, including bright yellow hyperkeratotic plates with erythematous fissures that covered his entire body like a collodion baby. Currently, he exhibited erythroderma, photosensitivity, ectropion, auricular pavilion alterations, and musculoskeletal disorders, such as equinovarus feet, fingers, hands, and hypoplastic feet with contractures in flexion and marked difficulty in fine motor skills. In addition, he presented dyschromatopsia, Achilles reflex hyporeflexia, slight speech, dental alteration and deficient cognitive performance. After the genetic sequencing, variants were found in ABCA12 and HRNR which are related to several skin diseases, including ichthyosis. Conclusions: Although in clinical practice, ichthyosis is a common entity, a severe type of ichthyosis is presented, highlighting the importance of appropriate genetic diagnosis, given the broad spectrum of genetic alterations with similar phenotypic and clinical characteristics. These pathologies must be known to guarantee initial support measures to prevent complications and offer multidisciplinary management to those patients. [ABSTRACT FROM AUTHOR]

Carnivore protoparvovirus 1 is one of the most important pathogens affecting both wild and domestic carnivores. Here, we reported the genetic characterization of canine parvovirus (CPV‐2) strains from a rescued guiña (Leopardus guigna) and domestic dogs from Chile. Guiña strain was classified as CPV‐2c, and phylogenetic analysis of the complete coding genome showed that the guiña CPV‐2c strain shares a recent common ancestor with Chilean domestic dogs' strains. These viruses showed >99% identity and exhibited three changes in the NS1 protein (V596A, E661K and L582F). This is the first detection and genetic characterization of CPV‐2c infection in guiña worldwide, and one of the few comparative studies that show the source of infection was domestic dogs. The current findings highlight the fact that guiña is a susceptible species to protoparvovirus infection and that domestic dogs represent an important threat to its conservation. The CPV‐2 cross‐species transmission between domestic dogs and guiña should be taken into account for protection programmes of this endangered species. [ABSTRACT FROM AUTHOR]

Infectious bursal disease virus (IBDV) is an economically relevant and widespread pathogen that produces immunosuppression in young chickens. IBDV is genetically classified into seven genogroups (G1–G7), where the traditional classic, variant and very virulent strains correspond to G1, G2 and G3, respectively. The G4 strains, also known as 'distinct' (dIBDV), have recently acquired increased relevance because of their prevalence and notorious impair to the poultry industry in South America. Here, worldwide dIBDV strains were studied using phylogenetic and phylodynamic approaches. The phylogenetic analyses performed using partial and complete sequences of both viral segments (A and B) consistently clustered the dIBDV strains in a monophyletic group. The analyses of the VP5, polyprotein and VP1 coding regions identified amino acid residues that act as markers for the identification of the entire dIBDV group or different sub‐populations. The phylodynamic analyses performed using the hypervariable region of VP2 indicated that the dIBDV strains emerged in the early 1930s in Eastern Europe, shortly after the emergence of classic strains (1927) and before variant (1949) and very virulent strains (1967). The analysis of the migration routes indicated that after its emergence, the dIBDV strains spread to Eastern Asia around 1959, to Brazil around 1963, and to Argentina around 1990. These inter‐continental migrations resulted in three sub‐populations that are currently represented by strains from (a) Brazil, (b) Eastern Asia and Canada, and (c) Eastern Europe, Argentina and Uruguay. Taken together, our results highlight the complex evolutionary history of IBDV and the importance of new phylodynamic data to unravel and nearly follow the different evolutionary pathways taken by this important poultry pathogen. [ABSTRACT FROM AUTHOR]

Infectious bronchitis virus (IBV) is a persistent sanitary problem for the South American poultry industry despite extensive vaccination. The IBV single-stranded RNA genome has high rates of mutation and recombination that generate a notorious virus variability. Since most IBV vaccines are type-specific, there is a need for constant surveillance of the circulating lineages and knowledge about their genetic and antigenic properties. Here we present an integrative analysis that provides the pattern of genetic variation of the South American IBV strains and information about their antigenic characteristics. The genetic analysis was performed using the S1 complete coding sequences of all available South American strains, including newly obtained Argentine and Uruguayan field samples. Our phylogenetic and phylodynamic analyses evidence that three main lineages (GI-1, GI-11 and GI-16) are extensively circulating in South American flocks. Strains of the GI-1 lineage (Massachusetts-type) were detected in Argentina, Brazil, Chile and Colombia. The GI-11 lineage is an exclusively South American lineage that emerged in the 1950s, and is the predominant lineage in Brazil and Uruguay at present. The GI-16 lineage emerged around 1979, and is currently circulating in most South American territories (Argentina, Chile, Uruguay, Colombia and Peru). The virus cross-neutralization test performed here reveals very low antigenic relatedness between GI-11 and GI-16 lineages (i.e. they are different serotypes). The results of this study extend our knowledge about the present and past IBV variability in South America and provide relevant elements to improve the control programmes by considering the genetic and antigenic attributes of IBV. [ABSTRACT FROM AUTHOR]

Infectious bursal disease virus (IBDV) is the causative agent of a highly contagious immunosuppressive disease affecting young chickens. The recently described "distinct IBDV" (dIBDV) genetic lineage encompasses a group of worldwide distributed strains that share conserved genetic characteristics in both genome segments making them unique within IBDV strains. Phenotypic characterization of these strains is scarce and limited to Asiatic and European strains collected more than 15 years ago. The present study aimed to assess the complete and comprehensive phenotypic characterization of a recently collected South American dIBDV strain (1/chicken/URY/1302/16). Genetic analyses of both partial genome segments confirmed that this strain belongs to the dIBDV genetic lineage and that it is not a reassortant. Antigenic analysis with monoclonal antibodies indicated that this strain has a particular antigenic profile, similar to that obtained in a dIBDV strain from Europe (80/GA), which differs from those previously found in the traditional classic, variant and very virulent strains. Chickens infected with the South American dIBDV strain showed subclinical infections but had a marked bursal atrophy. Further analysis using Newcastle disease virus-immunized chickens, previously infected with the South American and European dIBDV strains, demonstrated their severe immunosuppressive effect. These results indicate that dIBDV strains currently circulating in South America can severely impair the immune system of chickens, consequently affecting the local poultry industry. Our study provides new insights into the characteristics and variability of this global genetic lineage and is valuable to determine whether specific control measures are required for the dIBDV lineage. Research Highlights A South American strain of the dIBDV lineage was phenotypically characterized. The strain produced subclinical infections with a marked bursal atrophy. Infected chickens were severely immunosuppressed. The dIBDV strains are antigenically divergent from other IBDV lineages. [ABSTRACT FROM AUTHOR]

Anamnesis: a 4-year-old female dog‚ Pinscher breed‚ was presented to a small animal clinic in Colombia with a 2-month evolution of a skin and pruritic problem‚ alopecic skin lesions on the trunk and lesions with ulcers and crusts on the tips of the ears with serosanguineous discharge. Owner reported a previous treatment for scabies without a favorable response. Clinical findings: the canine patient presented round multifocal skin lesions on the trunk consistent with epidermal collarettes‚ as well as lesions with ulcers and crusts on the tips of the ears with serosanguinous discharge‚ consistent with ear tip vasculitis. The general examination of the patient was normal. Diagnostic: cutaneous histoplasmosis due to Histoplasma capsulatum was confirmed by cytology‚ histopathological analysis of skin biopsy that revealed structures consistent with fungal forms‚ Gomori-Grocott methenamine silver staining. For molecular diagnosis by nested PCR‚ DNA was extracted from skin and serum by E.Z.N.A.® Tissue DNA kit‚ and primers were designed to amplify 111 bp and 279 bp fragments from M antigen of H. capsulatum as a target. Amplicons were sequenced and confirmed as H. capsulatum by Sanger method. Treatment: after the diagnosis‚ the patient did not return for consultation‚ however‚ the treatment for histoplasmosis typically involves the use of an azole antifungal drug (e.g., ketoconazole‚ itraconazole‚ fluconazole‚ or posaconazole) which inhibits sterol 14α-demethylase‚ involved in ergosterol synthesis‚ a key component of the fungal cell wall. Results and conclusions: the diagnosis of cutaneous histoplasmosis in dogs can be difficult due to the resemblance of the intracellular structures to those of other pathogens. Therefore‚ it is important to confirm the diagnosis using complementary tests such as histopathology and PCR. To the authors’ knowledge‚ this is the first report of molecular detection of H. capsulatum as the causative agent of skin lesions in a canine patient in Colombia‚ emphasizing the need to consider this pathogen as a differential diagnosis in dogs with epidermal collarette-type lesions and/or lesions compatible with ear tip vasculitis. [ABSTRACT FROM AUTHOR]

In agricultural ecosystems, pest insects, pathogens, and reduced soil fertility pose major challenges to crop productivity and are responsible for significant yield losses worldwide. Management of belowground pests and diseases remains particularly challenging due to the complex nature of the soil and the limited reach of conventional agrochemicals. Boosting the presence of beneficial rhizosphere organisms is a potentially sustainable alternative and may help to optimize crop health and productivity. Field application of single beneficial soil organisms has shown satisfactory results under optimal conditions. This might be further enhanced by combining multiple beneficial soil organisms, but this remains poorly investigated. Here, we inoculated wheat plots with combinations of three beneficial soil organisms that have different rhizosphere functions and studied their effects on crop performance. Plant beneficial Pseudomonas bacteria, arbuscular mycorrhizal fungi (AMF), and entomopathogenic nematodes (EPN), were inoculated individually or in combinations at seeding, and their effects on plant performance were evaluated throughout the season. We used traditional and molecular identification tools to monitor their persistence over the cropping season in augmented and control treatments, and to estimate the possible displacement of native populations. In three separate trials, beneficial soil organisms were successfully introduced into the native populations and readily survived the field conditions. Various Pseudomonas, mycorrhiza, and nematode treatments improved plant health and productivity, while their combinations provided no significant additive or synergistic benefits compared to when applied alone. EPN application temporarily displaced some of the native EPN, but had no significant long-term effect on the associated food web. The strongest positive effect on wheat survival was observed for Pseudomonas and AMF during a season with heavy natural infestation by the frit fly, Oscinella frit, a major pest of cereals. Hence, beneficial impacts differed between the beneficial soil organisms and were most evident for plants under biotic stress. Overall, our findings indicate that in wheat production under the test conditions the three beneficial soil organisms can establish nicely and are compatible, but their combined application provides no additional benefits. Further studies are required, also in other cropping systems, to fine-tune the functional interactions among beneficial soil organisms, crops, and the environment. [ABSTRACT FROM AUTHOR]

Accurate determination of water depth is indispensable in multiple aspects of civil engineering (dock construction, dikes, submarines outfalls, trench control, etc.). To determine the type of atmospheric correction most appropriate for the depth estimation, different accuracies are required. Accuracy in bathymetric information is highly dependent on the atmospheric correction made to the imagery. The reduction of effects such as glint and cross-track illumination in homogeneous shallow-water areas improves the results of the depth estimations. The aim of this work is to assess the best atmospheric correction method for the estimation of depth in shallow waters, considering that reflectance values cannot be greater than 1.5% because otherwise the background would not be seen. This paper addresses the use of hyperspectral imagery to quantitative bathymetric mapping and explores one of the most common problems when attempting to extract depth information in conditions of variable water types and bottom reflectances. The current work assesses the accuracy of some classical bathymetric algorithms (Polcyn- Lyzenga, Philpot, Benny-Dawson, Hamilton, principal component analysis) when four different atmospheric correction methods are applied and water depth is derived. No atmospheric correction is valid for all type of coastal waters, but in heterogeneous shallow water the model of atmospheric correction 6S offers good results. [ABSTRACT FROM AUTHOR]

The infectious bursal disease virus (IBDV) is a major health threat to the world’s poultry industry despite intensive controls including proper biosafety practices and vaccination. IBDV (Avibirnavirus, Birnaviridae) is a non-enveloped virus with a bisegmented double-stranded RNA genome. The virus is traditionally classified into classic, variant and very virulent strains, each with different epidemiological relevance and clinical implications. Recently, a novel worldwide spread genetic lineage was described and denoted as distinct (d) IBDV. Here, we report the development and validation of a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay for the specific detection of dIBDVs in the global poultry industry. The assay employs a TaqMan-MGB probe that hybridizes with a unique molecular signature of dIBDV. The assay successfully detected all the assessed strains belonging to the dIBDV genetic lineage, showing high specificity and absence of cross-reactivity with non-dIBDVs, IBDV-negative samples and other common avian viruses. Using serial dilutions ofin vitro-transcribed RNA we obtained acceptable PCR efficiencies and determination coefficients, and relatively small intra- and inter-assay variability. The assay demonstrated a wide dynamic range between 103and 108RNA copies/reaction. This rapid, specific and quantitative assay is expected to improve IBDV surveillance and control worldwide and to increase our understanding of the molecular epidemiology of this economically detrimental poultry pathogen. [ABSTRACT FROM PUBLISHER]

We analyzed the main karyologic changes that have occurred during the dispersion of Triatoma infestans, the main vector of Chagas disease. We identified two allopatric groups, named Andean and non-Andean. The Andean specimens present C-heterochromatic blocks in most of their 22 chromosomes, whereas non-Andean specimens have only 4-7 autosomes with C-banding. These heterochromatin differences are the likely cause of a striking DNA content variation (approximately 30%) between Andean and non-Andean insects. Our study, together with previous historical and genetic data, suggests that T. infestans was originally a sylvatic species, with large quantities of DNA and heterochromatin, inhabiting the Andean region of Bolivia. However, the spread of domestic T. infestans throughout the non-Andean regions only involved insects with an important reduction of heterochromatin and DNA amounts. We propose that heterochromatin and DNA variation mainly reflected adaptive genomic changes that contribute to the ability of T. infestans to survive, reproduce, and disperse in different environments. [ABSTRACT FROM AUTHOR]

Background: Campylobacter fetus is a pathogen of major concern for animal and human health. The species shows a great intraspecific variation, with three subspecies: C. fetus subsp. fetus, C. fetus subsp. venerealis, and C. fetus subsp. testudinum. Campylobacter fetus fetus affects a broad range of hosts and induces abortion in sheep and cows. Campylobacter fetus venerealis is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus testudinum has been proposed recently based on genetically divergent strains isolated from reptiles and humans. Both C. fetus fetus and C. fetus testudinum are opportunistic pathogens for immune-compromised humans. Biochemical tests remain as the gold standard for identifying C. fetus but the fastidious growing requirements and the lack of reliability and reproducibility of some biochemical tests motivated the development of molecular diagnostic tools. These methods have been successfully tested on bovine isolates but fail to detect some genetically divergent strains isolated from other hosts. The aim of the present study was to develop a highly specific molecular assay to identify and quantify C. fetus strains. Results: We developed a highly sensitive real-time PCR assay that targets a unique region of the 16S rRNA gene. This assay successfully detected all C. fetus strains, including those that were negative for the cstA gene-based assay used as a standard for molecular C. fetus identification. The assay showed high specificity and absence of cross-reactivity with other bacterial species. The analytical testing of the assay was determined using a standard curve. The assay demonstrated a wide dynamic range between 102 and 107 genome copies per reaction, and a good reproducibility with small intra- and inter-assay variability. Conclusions: The possibility to characterize samples in a rapid, sensitive and reproducible way makes this assay a good option to establish a new standard in molecular identification and quantification of C. fetus species. [ABSTRACT FROM AUTHOR]

Background: Campylobacter fetus is a pathogen of major concern for animal and human health. The species shows a great intraspecific variation, with three subspecies: C. fetus subsp. fetus, C. fetus subsp. venerealis, and C. fetus subsp. testudinum. Campylobacter fetus fetus affects a broad range of hosts and induces abortion in sheep and cows. Campylobacter fetus venerealis is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus testudinum has been proposed recently based on genetically divergent strains isolated from reptiles and humans. Both C. fetus fetus and C. fetus testudinum are opportunistic pathogens for immune-compromised humans. Biochemical tests remain as the gold standard for identifying C. fetus but the fastidious growing requirements and the lack of reliability and reproducibility of some biochemical tests motivated the development of molecular diagnostic tools. These methods have been successfully tested on bovine isolates but fail to detect some genetically divergent strains isolated from other hosts. The aim of the present study was to develop a highly specific molecular assay to identify and quantify C. fetus strains. Results: We developed a highly sensitive real-time PCR assay that targets a unique region of the 16S rRNA gene. This assay successfully detected all C. fetus strains, including those that were negative for the cstA gene-based assay used as a standard for molecular C. fetus identification. The assay showed high specificity and absence of cross-reactivity with other bacterial species. The analytical testing of the assay was determined using a standard curve. The assay demonstrated a wide dynamic range between 102 and 107 genome copies per reaction, and a good reproducibility with small intra- and inter-assay variability. Conclusions: The possibility to characterize samples in a rapid, sensitive and reproducible way makes this assay a good option to establish a new standard in molecular identification and quantification of C. fetus species. [ABSTRACT FROM AUTHOR]

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Infectious bursal disease virus (IBDV) is one of the most concerning health problems for world poultry production. IBDVs comprise four well-defined evolutionary lineages known as classic (c), classic attenuated (ca), variant (va) and very virulent (vv) strains. Here, we characterized IBDVs from South America by the genetic analysis of both segments of the viral genome. Viruses belonging to c, ca and vv strains were unambiguously classified by the presence of molecular markers and phylogenetic analysis of the hypervariable region of thevp2gene. Notably, the majority of the characterized viruses (9 out of 15) could not be accurately assigned to any of the previously described strains and were then denoted as distinct (d) IBDVs. These dIBDVs constitute an independent evolutionary lineage that also comprises field IBDVs from America, Europe and Asia. The hypervariable VP2 sequence of dIBDVs has a unique and conserved molecular signature (272T, 289P, 290I and 296F) that is a diagnostic character for classification. A discriminant analysis of principal components (DAPC) also identified the dIBDVs as a cluster of genetically related viruses separated from the typical strains. DAPC and genetic distance estimation indicated that the dIBDVs are one of the most genetically divergent IBDV lineages. Thevp1gene of the dIBDVs has non-vvIBDV markers and unique nucleotide and amino acid features that support their divergence in both genomic segments. The present study suggests that the dIBDVs comprise a neglected, highly divergent lineage that has been circulating in world poultry production since the early time of IBDV emergence. [ABSTRACT FROM AUTHOR]

The objective of the experiment was to compare the use of a PGF2α analogue (Cloprostenol) IM, with an intravaginal progestagen sponge, flurogestone acetate (FGA), and equine chorionic gonadotropin (eCG) IM application protocol. A total of 30 cyclical hair ewes (54.07 ± 0.5 kg live weight, body condition score 3.5 ± 0.5, and age 3 ± 1 years) were used. For the control group ewes ( n = 15), intravaginal sponges (IS) impregnated with 20 mg of FGA were inserted for 12 days with 500 IU of eCG IM at sponges withdrawal. For the PG group ewes (Treatment group n = 15), two injections of Cloprostenol (75 mcg) were given 12 days apart. The presence of estrus was detected using two rams with 8 h interval beginning at the end of the treatment. Progesterone concentrations in blood were measured by solid phase radioimmunoassay. A student's t test was performed to analyze the duration of estrus and the interval between the ends of the treatment and the onset of estrus (ET-OE) presentation. Progesterone levels were compared with two-way ANOVA, with treatment, and day of menstrual cycle as fixed factors. Treatment costs ratio was calculated by dividing the total costs of FGA IS application between total costs of Cloprostenol application. Significant differences ( P < 0.05) were found in the (ET-OE) interval and estrus duration. For the control group, estrus was presented at 30 + 8.2 h; in treatment group, at 44 h after the last application, duration of estrus was 54.9 + 8.34 h, and 41 + 1.83 h for the control and treatment group, pregnancy rates were 53.3 and 60.0 %, respectively. Significant differences ( P < 0.001) were found from days 9 to 13 on Progesterone levels in both treatments. Treatment costs of Cloprostenol protocol were 2.63 cheaper than FGA including disposable material, biological products, and labor. It was concluded that Cloprostenol could be an effective tool in estrus synchronization in hair sheep in tropical areas. [ABSTRACT FROM AUTHOR]

Canine parvovirus (CPV), a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c) with different frequencies and genetic variability among countries. The contribution of co-infection and recombination to the genetic variability of CPV is far from being fully elucidated. Here we took advantage of a natural CPV population, recently formed by the convergence of divergent CPV-2c and CPV-2a strains, to study co-infection and recombination. Complete sequences of the viral coding region of CPV-2a and CPV-2c strains from 40 samples were generated and analyzed using phylogenetic tools. Two samples showed co-infection and were further analyzed by deep sequencing. The sequence profile of one of the samples revealed the presence of CPV-2c and CPV-2a strains that differed at 29 nucleotides. The other sample included a minor CPV-2a strain (13.3% of the viral population) and a major recombinant strain (86.7%). The recombinant strain arose from inter-genotypic recombination between CPV-2c and CPV-2a strains within the VP1/VP2 gene boundary. Our findings highlight the importance of deep-sequencing analysis to provide a better understanding of CPV molecular diversity. [ABSTRACT FROM AUTHOR]

The genus Campylobacter includes some of the most relevant pathogens for human and animal health; the continuous effort in their characterization has also revealed new species putatively involved in different kind of infections. Nowadays, the available genomic data for the genus comprise a wide variety of species with different pathogenic potential and niche preferences. In this work, we contribute to enlarge this available information presenting the first genome for the species Campylobacter sputorum bv. sputorum and use this and the already sequenced organisms to analyze the emergence and evolution of pathogenicity and niche preferences among Campylobacter species. We found that campylobacters can be unequivocally distinguished in established and putative pathogens depending on their repertory of virulence genes, which have been horizontally acquired from other bacteria because the nonpathogenic Campylobacter ancestor emerged, and posteriorly interchanged between some members of the genus. Additionally, we demonstrated the role of both horizontal gene transfers and diversifying evolution in niche preferences, being able to distinguish genetic features associated to the tropism for oral, genital, and gastrointestinal tissues. In particular, we highlight the role of nonsynonymous evolution of disulphide bond proteins, the invasion antigen B (CiaB), and other secreted proteins in the determination of niche preferences. Our results arise from assessing the previously unmet goal of considering the whole available Campylobacter diversity for genome comparisons, unveiling notorious genetic features that could explain particular phenotypes and set the basis for future research in Campylobacter biology. [ABSTRACT FROM AUTHOR]

Canine distemper virus (CDV, Paramyxoviridae, Morbillivirus) is the causative agent of a severe infectious disease affecting terrestrial and marine carnivores worldwide. Phylogenetic relationships and the genetic variability of the hemagglutinin (H) protein and the fusion protein signal-peptide (Fsp) allow for the classification of field strains into genetic lineages. Currently, there are nine CDV lineages worldwide, two of them co-circulating in South America. Using the Fsp-coding region, we analyzed the genetic variability of strains from Uruguay, Brazil, and Ecuador, and compared them with those described previously in South America and other geographical areas. The results revealed that the Brazilian and Uruguayan strains belong to the already described South America lineage (EU1/SA1), whereas the Ecuadorian strains cluster in a new clade, here named South America 3, which may represent the third CDV lineage described in South America. [ABSTRACT FROM AUTHOR]

The Rhodnius Pacific group is composed of three species: Rhodnius pallescens, R. colombiensis and R. ecuadoriensis, which are considered important vectors of trypanosomes (Trypanosoma cruzi and T. rangeli) infecting humans. This group is considered as a recent trans-Andean lineage derived from the widespread distributed sister taxa R. pictipes during the later uplift of northern Andes mountain range. The widest spread species R. pallescens may be a complex of two divergent lineages with different chromosomal attributes and a particular biogeographical distribution across Central America and Colombia with several southern populations in Colombia occupying the same sylvatic habitat as its sister species R. colombiensis. Although the taxonomy of Rhodnius Pacific group has been well studied, the unresolved phylogenetic and systematic issues are the target of this paper. Here we explore the molecular phylogeography of this species group analyzing two mitochondrial (ND4 and cyt b) and one nuclear (D2 region of ribosomal 28S gene) gene sequences. The molecular analyses suggest an early divergence of the species R. ecuadoriensis and R. colombiensis, followed by a recent expansion of R. pallescens lineages. The phylogenetic relationship between sympatric R. pallescens Colombian lineage and R. colombiensis was further explored using wing morphometry, DNA genome size measurements, and by analyzing chromosomal behavior of hybrids progeny obtained from experimental crosses. Our results suggest that the diversification of the two R. pallescens lineages was mainly influenced by biogeographical events such as (i) the emergence of the Panama Isthmus, while the origin and divergence of R. colombiensis was associated with (ii) the development of particular genetic and chromosomal features that act as isolation mechanisms from its sister species R. pallescens (Colombian lineage). These findings provide new insights into the evolution of the Rhodnius Pacific group and the underlying biological processes that occurred during its divergence. [ABSTRACT FROM AUTHOR]

Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) with different frequencies and genetic variability among countries. Current CPV populations are considered to be spatially structured with relatively little movement of viruses between geographical areas. Here we describe the evolution and population dynamics of CPV in Uruguay from 2006-2011 using full-length capsid viral protein 2 (VP2) sequences. CPV-2c was the predominant variant in Uruguay for 4 years (2006-2009). The estimated time to the most recent common ancestor suggested that the CPV-2c variant appeared in Uruguay around 2004-2005. Comparative phylogenetic analysis revealed that South American CPV-2c strains did not emerge de novo but may have a European origin. In 2010, a remarkable epidemiological change occurred as a consequence of the emergence of a novel CPV-2a strain in the previously homogeneous CPV-2c population. The frequency of the novel CPV-2a strain increased to 85 % in 2011, representing the first example of a CPV-2a strain replacing a predominant CPV-2c strain in a dog population. The CPV-2a strains detected in 2010-2011 were not phylogenetically related to any other strain collected on the American continent but were identical to Asiatic strains, suggesting that its emergence was a consequence of a migration event. Taken together, our findings suggest that in the last decade, Uruguay has experienced two successive invasions by CPV-2c and CPV-2a variants of European and Asiatic origins, respectively. These results support the hypothesis that CPV invasion events are not rare in certain geographic regions and indicate that some current strains may exhibit an unexpectedly high invasion and replacement capability. [ABSTRACT FROM AUTHOR]

Canine distemper virus (CDV; Paramyxoviridae, Morbillivirus) is the etiologic agent of a multisystemic infectious disease affecting all terrestrial carnivore families with high incidence and mortality in domestic dogs. Sequence analysis of the hemagglutinin (H) gene has been widely employed to characterize field strains, permitting the identification of nine CDV lineages worldwide. Recently, it has been established that the sequences of the fusion protein signal-peptide (Fsp) coding region are extremely variable, suggesting that analysis of its sequence might be useful for strain characterization studies. However, the divergence of Fsp sequences among worldwide strains and its phylogenetic resolution has not yet been evaluated. We constructed datasets containing the Fsp-coding region and H gene sequences of the same strains belonging to eight CDV lineages. Both datasets were used to evaluate their phylogenetic resolution. The phylogenetic analysis revealed that both datasets clustered the same strains into eight different branches, corresponding to CDV lineages. The inter-lineage amino acid divergence was fourfold greater for the Fsp peptide than for the H protein. The likelihood mapping revealed that both datasets display strong phylogenetic signals in the region of well-resolved topologies. These features indicate that Fsp-coding region sequence analysis is suitable for evolutionary studies as it allows for straightforward identification of CDV lineages. [ABSTRACT FROM AUTHOR]

α-Actinin, an actin-binding protein of the spectrin superfamily, is present in most eukaryotes except plants. It is composed of three domains: N-terminal CH-domains, C-terminal calcium-binding domain (with EF-hand motifs), and a central rod domain. We have cloned and expressed Neurospora crassa α-actinin as GST and GFP fusion proteins for biochemical characterization and in vivo localization, respectively. The intracellular localization pattern of α-actinin suggests that this protein is intimately associated with actin filaments and plays an important role in the processes of germination, hyphal elongation, septum formation, and conidiation. These functions were confirmed by the experiments on the effect of α-actinin gene deletion in N. crassa. [ABSTRACT FROM AUTHOR]

The infectious bursal disease virus (IBDV; Birnaviridae family) constitutes one of the main threats to the poultry industry worldwide. Most of the progress in the molecular epidemiology of this virus has been achieved through the study of the coding region of the capsid protein VP2. Little research has been done regarding the molecular evolution and the epidemiological implications of genetic variability of other IBDV genome regions. In this article, the gene that codes the non-structural protein VP5 was analyzed. Although this protein is not essential for the virus replication, recent evidence indicates that it could be related to the virulent phenotype and the adaptive capacity of the virus. The VP5 gene is also of evolutionary interest because it has an open reading frame that terminally overlaps with the pVP2–VP4–VP3 polyprotein coding region. In the first part of this study, the full VP5 gene of a South American strain was characterized. The results revealed that the VP5 gene of Uruguayan hypervirulent IBDV strains (vvIBDV) lacks the alternative AUG start codon characteristic of the vvIBDV strains that have been described to date. Instead, as occurs in classic and variant strains, this VP5 gene has an AUG start site located four codons downstream and, consequently, it codes for a 145 amino acid long protein rather than the putative 149 amino acid long protein of other vvIBDV. In spite of this, these viruses conserved the VP5 and VP2 amino acid signature of the hypervirulent strains and clustered with reference vvIBDV sequences. This finding may represent evidence that the VP5 gene could be evolving by changing the translation initiation site. In the second part of this study, an evolutionary analysis including the sequences reported in this study together with most of VP5 sequences available in the GenBank, showed the existence of a complex system of selective pressures controlling the evolution of the VP5 gene. Using the d N/d S index, we found a strong purifying selection exerted on the 5′ terminal overlapping region of VP2 that would be constraining the evolution of VP5. These results reinforce the hypothesis that the VP5 gene was originated late in the IBDV evolution by a mechanism of genetic overprinting. The results described in this study provided new information about the dynamics of the IBDV genome and revealed some of the mechanisms at play in the evolution of this virus. Since VP5 seems to be related to viral pathogenicity, this evolutionary information might be useful to highlight the impact of the genetic variation of this protein on the epidemiology of IBDV. [ABSTRACT FROM AUTHOR]

The meiotic behaviour of the X chromosome and one autosomal pair of the heteropteran Triatoma infestans was analysed by means of C-banding plus DAPI staining. At first metaphase, the X univalent is oriented with its long axis parallel to the equatorial plate, which suggests a holocentric interaction with the spindle fibres. After this initial orientation, kinetic activity is restricted to one of both chromatid ends. The election of the active chromatid end is random and it is independent of the end selected in the sister chromatid. At second metaphase, the X and Y chromatids associate side by side forming a pseudobivalent. After that, the kinetic activity is again restricted to either of both chromosomal ends in a random fashion. At first metaphase, the fourth autosomal bivalent shows two alternative random orientations depending on the chromosome end showing kinetic activity (DAPI positive or opposite). At second metaphase, half bivalents are oriented with their long axis parallel to the equatorial plate. Three different segregation patterns are observed. The kinetic activity can be localised: (i) in the end with the DAPI signal (46.9%), (ii) in the opposite end (44.6%) or (iii) in one DAPI-positive end in one chromatid and in the opposite end in the other one (8.5%). The existence of the last pattern indicates that the same end can show kinetic activity during both meiotic divisions. Our results provide new information on the comparative meiotic behaviour of autosomes and sex chromosomes in holocentric systems. [ABSTRACT FROM AUTHOR]

Accurate determination of water depth is indispensable in multiple aspects of civil engineering (dock construction, dikes, submarines outfalls, trench control, etc.). According to the final objective, different accuracies will be required. Accuracy in bathymetric information is highly dependent on the atmospheric correction made to the imagery. The reduction of effects such as glint and cross track illumination in shallow-water areas with homogeneous improves the results of the depth estimations. The aim of this work is to assess the best atmospheric correction method for the estimation of depth in shallow waters. This paper addresses the use of hyperspectral imagery to quantitative bathymetric mapping, and explores one of the most common problems when attempting to extract depth information in conditions of variable water types and bottom reflectances. The current work assesses the accuracy of some classical bathymetric algorithms (Polcyn-Lyzenga, Philpot, Benny-Dawson, Hamilton, Principal Component Analysis) when four different atmospheric correction methods are applied and water depth is derived. This work shows the importance of atmospheric correction in order to depth estimation in shallow waters. None atmospheric correction is valid for all type of coastal waters but in heterogeneous shallow water, the model of atmospheric correction 6S offers good results. [ABSTRACT FROM AUTHOR]