Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks.

Equine herpesvirus 1 (EHV-1) causes respiratory disease, abortion, neonatal death and neurological disease in equines and is endemic in most countries. The viral factors that influence EHV-1 disease severity are poorly understood, and this has hampered vaccine development. However, the N752D substitution in the viral DNA polymerase catalytic subunit has been shown statistically to be associated with neurological disease. This has given rise to the term "neuropathic strain," even though strains lacking the polymorphism have been recovered from cases of neurological disease. To broaden understanding of EHV-1 diversity in the field, 78 EHV-1 strains isolated over a period of 35 years were sequenced. The great majority of isolates originated from the United Kingdom and included in the collection were low passage isolates from respiratory, abortigenic and neurological outbreaks. Phylogenetic analysis of regions spanning 80% of the genome showed that up to 13 viral clades have been circulating in the United Kingdom and that most of these are continuing to circulate. Abortion isolates grouped into nine clades, and neurological isolates grouped into five. Most neurological isolates had the N752D substitution, whereas most abortion isolates did not, although three of the neurological isolates from linked outbreaks had a different polymorphism. Finally, bioinformatic analysis suggested that recombination has occurred between EHV-1 clades, between EHV-1 and equine herpesvirus 4, and between EHV-1 and equine herpesvirus 8.

Prevalence of mixed genotype hepatitis C virus infections in the UK as determined by genotype-specific PCR and deep sequencing.

The incidence of mixed genotype hepatitis C virus (HCV) infections in the UK is largely unknown. As the efficacy of direct-acting antivirals is variable across different genotypes, treatment regimens are tailored to the infecting genotype, which may pose issues for the treatment of underlying genotypes within undiagnosed mixed genotype HCV infections. There is therefore a need to accurately diagnose mixed genotype infections prior to treatment. PCR-based diagnostic tools were developed to screen for the occurrence of mixed genotype infections caused by the most common UK genotypes, 1a and 3, in a cohort of 506 individuals diagnosed with either of these genotypes. The overall prevalence rate of mixed infection was 3.8%; however, this rate was unevenly distributed, with 6.7% of individuals diagnosed with genotype 3 harbouring genotype 1a strains and only 0.8% of samples from genotype 1a patients harbouring genotype 3 (P < .05). Mixed infection samples consisted of a major and a minor genotype, with the latter constituting less than 21% of the total viral load and, in 67% of cases, less than 1% of the viral load. Analysis of a subset of the cohort by Illumina PCR next-generation sequencing resulted in a much greater incidence rate than obtained by PCR. This may have occurred due to the nonquantitative nature of the technique and despite the designation of false-positive thresholds based on negative controls.

Bioinformatics tools for analysing viral genomic data.

The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing.

Le champ de la génomique virale et de la bio-informatique connaît actuellement un nouvel essor grâce à la technologie du séquençage à haut débit (SHD), qui permet de séquencer puis d'assembler rapidement un très grand nombre de génomes viraux, à un coût abordable. De surcroît, grâce à la puissance sans précédent des technologies du SHD, il est désormais possible d'analyser la diversité des virus au sein d'un hôte ainsi que la dynamique des quasi-espèces afin d'élucider d'importantes questions biologiques ayant trait à la transmission virale, à la résistance vis-à-vis des vaccins et au passage d'un hôte à l'autre. Le SHD permet également d'identifier rapidement des virus connus ou potentiellement nouveaux dans des échantillons de terrain ou cliniques, ce qui apporte de nouveaux outils pour la découverte des virus et la métagénomique. La bio-informatique joue un rôle central dans le développement des applications du SHD car ce domaine en constante évolution génère des séries de données aussi nombreuses que complexes dont le traitement et l'analyse requièrent en permanence de nouveaux algorithmes et logiciels. Les auteurs font rapidement le point sur les principaux outils de la bio-informatique utilisés dans la recherche sur les génomes viraux, en mettant particulièrement l'accent sur les technologies du SHD et sur leurs applications les plus importantes. Ils décrivent schématiquement les grandes étapes de différents types d'analyse recourant au SHD, depuis le contrôle qualité des lectures brutes jusqu'aux activités telles que l'assemblage de séquences consensus et de novo du génome, l'appel de variants et la métagénomique, et enfin le séquençage d'ARN.

El campo de la genómica vírica y la bioinformática conoce hoy un renovado dinamismo gracias a las técnicas de secuenciación de alto rendimiento, que permiten secuenciar con rapidez y rentabilidad, y a continuación ensamblar, un gran número de genomas víricos. Además, la potencia sin precedentes que ofrecen estas técnicas ha hecho posible analizar la diversidad vírica dentro de los anfitriones y la dinámica de cuasiespecies en relación con importantes interrogantes biológicos tocantes a la transmisión de virus, la resistencia a las vacunas o el salto de un anfitrión a otro. Con la secuenciación de alto rendimiento también es posible identificar con celeridad los virus tanto conocidos como eventualmente nuevos que estén presentes en muestras clínicas u obtenidas sobre el terreno, lo que aporta nuevas herramientas al arsenal disponible en los campos del descubrimiento de virus y la metagenómica. La bioinformática ha sido un factor capital en el auge de las aplicaciones de técnicas de secuenciación de alto rendimiento, pues continuamente se necesitan nuevos algoritmos y programas informáticos para procesar y analizar los vastos y complejos conjuntos de datos que se generan en un ámbito sujeto a tan rápida evolución. Los autores repasan brevemente las principales herramientas bioinformáticas que existen para la investigación en genómica vírica, prestando especial atención a las técnicas de secuenciación de alto rendimiento y sus principales aplicaciones. Asimismo, resumen las etapas básicas de diversos procedimientos de análisis por secuenciación de alto rendimiento, empezando por el control de calidad de las lecturas brutas y pasando por labores que van desde el ensamblaje del genoma con creación de secuencia consenso o ensamblaje de novo hasta la asignación de variantes (variant calling) o la metagenómica, sin olvidar la secuenciación de ARN.

Immunity, homing and efficacy of allogeneic adoptive immunotherapy for posttransplant lymphoproliferative disorders.

Adoptive immunotherapy using autologous Epstein-Barr virus (EBV)-specific cytotoxic T-lymphocytes (auto-CTL) can regress posttransplant lymphoproliferative disorders (PTLD). Widespread applicability of auto-CTL remains constrained. Generation is time-consuming, and auto-CTL cannot be established in patients treated with the B-cell depleting antibody rituximab. By contrast, pregenerated allogeneic CTL (allo-CTL) offers immediate accessibility. Allo-CTL has previously shown efficacy in "early" polyclonal- PTLD. We treated three patients with aggressive, advanced monoclonal-PTLD following solid-organ transplantation. All were refractory to at least three prior therapies. Despite HLA disparity, there was negligible toxicity, with early in vivo antiviral efficacy and reconstitution of EBV peptide-specific immunity. Two patients attained complete remission (CR). One remains in CR 17 months following therapy, coincident with persistence of donor-derived tumor targeted EBV-specific CTL; the other died of non-PTLD related pathology. In the third patient, autopsy demonstrated homing of allo-CTL at the tumor site. Larger prospective studies of EBV-specific allo-CTL in PTLD are warranted.

Validation of an in vitro method to determine infectivity of cryopreserved sporozoites in stabilates of Theileria spp.

The infectivity of 15 cryopreserved Theileria spp. sporozoite stabilates was assessed semi-quantitatively by titration using naive peripheral blood mononuclear cells (PBM) in vitro in multi-well plates. Using the method described, the effective dilution, which would result in 50% of replicate wells infected (ED50), was calculated. The ED50 for 11 Theileria annulata stabilates in bovine PBM ranged from 10(-2.6) to 10(-4.2) dilutions of 1 tick equivalent (t.e.) ml(-1), one stabilate of Theileria parva 10(-2.2)t.e.ml(-1); and three Theileria lestoquardi stabilates in ovine PBM, from 10(-1.5) to 10(-1.8)t.e.ml(-1). Two of the T. annulata stabilates had been used individually to infect groups of calves: stabilate 52 produced more severe disease responses than stabilate 67, as measured by prepatent period, parasitosis, parasitaemia and death or recovery. This corresponded with the sixfold difference found in vitro between the ED50's of these two stabilates. This method is useful not only to measure the infection potential of the sporozoite stabilates but also as an in vitro model for chemotherapeutic and immunological studies of the early stages of theileriosis.

Complete regression of posttransplant lymphoproliferative disease using partially HLA-matched Epstein Barr virus-specific cytotoxic T cells.

BACKGROUND: Adoptive immunotherapy with autologous and donor-derived cytotoxic T lymphocytes (CTL) has recently been used to treat Epstein Barr virus (EBV)-positive posttransplant lymphoproliferative disease (PTLD). METHODS AND RESULTS: We report complete regression of EBV-positive PTLD in an 18-month-old small bowel and liver transplant recipient after one infusion of partially human leukocyte antigen (HLA)-matched EBV-specific CTL grown ex vivo from an EBV seropositive unrelated blood donor. No infusion-related toxicity or evidence of graft-versus-host disease was observed. The tumor showed signs of regression within 1 week and EBV load in peripheral blood dropped to undetectable levels. Limiting dilution analyses (LDA) detected no EBV-specific CTL precursor (CTLp) cells before the infusion, and high numbers of CTLp at 4 hr and 24 hr post-CTL infusion. There was a reversal of the CD4/8 ratio in peripheral blood and an increase in HLA-DR positive CD8 cells. The patient has been in complete remission for 24 months. CONCLUSION: If this success is repeated in more PTLD patients, then stored CTL could be used for antiviral and antitumor therapies in immunocompromised patients.

Drosophila wingless and pair-rule transcripts localize apically by dynein-mediated transport of RNA particles.

Asymmetric mRNA localization targets proteins to their cytoplasmic site of function. We have elucidated the mechanism of apical localization of wingless and pair-rule transcripts in the Drosophila blastoderm embryo by directly visualizing intermediates along the entire path of transcript movement. After release from their site of transcription, mRNAs diffuse within the nucleus and are exported to all parts of the cytoplasm, regardless of their cytoplasmic destinations. Endogenous and injected apical RNAs assemble selectively into cytoplasmic particles that are transported apically along microtubules. Cytoplasmic dynein is required for correct localization of endogenous transcripts and apical movement of injected RNA particles. We propose that dynein-dependent movement of RNA particles is a widely deployed mechanism for mRNA localization.

Merlin, the Drosophila homologue of neurofibromatosis-2, is specifically required in posterior follicle cells for axis formation in the oocyte.

In Drosophila, the formation of the embryonic axes is initiated by Gurken, a transforming growth factor alpha signal from the oocyte to the posterior follicle cells, and an unknown polarising signal back to the oocyte. We report that Drosophila Merlin is specifically required only within the posterior follicle cells to initiate axis formation. Merlin mutants show defects in nuclear migration and mRNA localisation in the oocyte. Merlin is not required to specify posterior follicle cell identity in response to the Gurken signal from the oocyte, but is required for the unknown polarising signal back to the oocyte. Merlin is also required non-autonomously, only in follicle cells that have received the Gurken signal, to maintain cell polarity and limit proliferation, but is not required in embryos and larvae. These results are consistent with the fact that human Merlin is encoded by the gene for the tumour suppressor neurofibromatosis-2 and is a member of the Ezrin-Radixin-Moesin family of proteins that link actin to transmembrane proteins. We propose that Merlin acts in response to the Gurken signal by apically targeting the signal that initiates axis specification in the oocyte.

Perturbing nuclear transport in Drosophila eye imaginal discs causes specific cell adhesion and axon guidance defects.

To study nucleocytoplasmic transport during multicellular development, we developed a sensitive nuclear protein import assay in living blastoderm embryos. We show that dominant negative truncations of the human nuclear transport receptor karyopherinbeta/Importinbeta (DNImpbeta) disrupt mRNA export and protein import in Drosophila. To test the sensitivity of different developmental processes to nuclear trafficking perturbations, we expressed DNImpbeta behind the morphogenetic furrow of the eye disc, at a time when photoreceptors are patterned and project their axons to the brain. DNImpbeta expression does not disrupt the correct specification of different photoreceptors, but causes a defect in cell adhesion that leads to some photoreceptors descending below the layer of ommatidia. The photoreceptors initially project their axons correctly to the posterior, but later their axons are unable to enter the optic stalk en route to the brain and continue to project an extensive network of misguided axons. The axon guidance and cell adhesion defects are both due to a disruption in the function of Ketel, the Drosophila ortholog of Importinbeta. We conclude that cell adhesion and axon guidance in the eye have specific requirements for nucleocytoplasmic transport, despite involving processes that occur primarily at the cell surface.

small bristles is required for the morphogenesis of multiple tissues during Drosophila development.

We found that mutations in small bristles (sbr) affect several tissues during the development of the fruit fly. In sbr embryos, neurons have defects in pathfinding and the body wall muscles have defective morphology. As adults, sbr flies have smaller and thinner bristles with a reduced diameter, suggesting a defective cytoskeleton within. The phenotypes we observe are consistent with defects in cell morphogenesis. We identified DmNXF1, the Drosophila homolog of a mRNA export protein that has been characterized in human (NXF1/TAP) and yeast (Mex67p) as the protein encoded by the small bristles locus. Given that a global decrease in mRNA export in these mutants is likely, the phenotypes we observe suggest that certain tissues are acutely sensitive to lower levels of cytoplasmic mRNA and the resultant decrease in protein synthesis during key stages of cellular morphogenesis.

Small bristles, the Drosophila ortholog of NXF-1, is essential for mRNA export throughout development.

We identified a temperature-sensitive allele of small bristles (sbr), the Drosophila ortholog of human TAP/NXF-1 and yeast Mex67, in a screen for mutants defective in mRNA export. We show that sbr is essential for the nuclear export of all mRNAs tested in a wide range of tissues and times in development. High resolution and sensitive in situ hybridization detect the rapid accumulation of individual mRNA species in sbr mutant nuclei in particles that are distinct from nascent transcript foci and resemble wild-type export intermediates. The particles become more numerous and intense with increasing time at the restrictive temperature and are exported very rapidly after shifting back to the permissive temperature. The mRNA export block is not due indirectly to a defect in splicing, nuclear protein import, or aberrant nuclear ultrastructure, suggesting that in sbr mutants, mRNA is competent for export but fails to dock or translocate through NPCs. We conclude that NXF-1 is an essential ubiquitous export factor for all mRNAs throughout development in higher eukaryotes.

Temporary uniocular blindness and ophthalmoplegia associated with a mandibular block injection. A case report.

A mandibular block injection produced temporary uniocular blindness, total ophthalmoplegia, mydriasis, and ptosis of the eyelid, with diplopia developing as the sight returned. These effects lasted 25-30 minutes. The explanation offered as to the cause of the anaesthetic phenomenon is an intra-arterial injection into the maxillary artery with backflow of anaesthetic solution into the middle meningeal artery. The instantaneous blindness results from the anaesthetic agent being carried into the central artery of the retina through an anastomosis of the ophthalmic and middle meningeal arteries via the recurrent meningeal branch of the lacrimal artery. Although of short duration, the symptoms mimic a more serious carotid artery embolus occluding the ophthalmic artery. Complications of mandibular blocks have been reported in the literature, however total blindness and ophthalmoplegia are extremely rare. This case report highlights an event where individual anatomical variation of the maxillary and middle meningeal arteries has allowed anaesthetic solution to be delivered to an ectopic site.

Exceptionally potent inhibitors of fatty acid amide hydrolase: the enzyme responsible for degradation of endogenous oleamide and anandamide.

The development of exceptionally potent inhibitors of fatty acid amide hydrolase (FAAH), the enzyme responsible for the degradation of oleamide (an endogenous sleep-inducing lipid), and anandamide (an endogenous ligand for cannabinoid receptors) is detailed. The inhibitors may serve as useful tools to clarify the role of endogenous oleamide and anandamide and may prove to be useful therapeutic agents for the treatment of sleep disorders or pain. The combination of several features-an optimal C12-C8 chain length, pi-unsaturation introduction at the corresponding arachidonoyl Delta(8,9)/Delta(11,12) and oleoyl Delta(9,10) location, and an alpha-keto N4 oxazolopyridine with incorporation of a second weakly basic nitrogen provided FAAH inhibitors with K(i)s that drop below 200 pM and are 10(2)-10(3) times more potent than the corresponding trifluoromethyl ketones.

Reciprocal cross-protection induced by sporozoite antigens SPAG-1 from Theileria annulata and p67 from Theileria parva.

Theileria annulata and Theileria parva both possess a major surface antigen on the sporozoite stage of the life-cycle, called SPAG-1 and p67, respectively. In each case, these antigens are vaccine candidates and have been shown to induce a degree of homologous protection in earlier work. These antigens share sequence homology and are serologically cross-reactive. Here, we confirm that these antigens confer protection against homologous species challenge. More importantly, they mutually confer a degree of cross-species protection raising the prospect of a common vaccine in the future.

Transcribed genes are localized according to chromosomal position within polarized Drosophila embryonic nuclei.

When some genes are silenced, their positions within the nucleus can change dramatically [1] [2]. It is unclear, however, whether genes move to new positions when they are activated [3]. The chromosomes within the polarized nuclei of the fruit fly Drosophila have a well-characterized apical-basal orientation (the Rabl configuration [4]). Using a high-resolution in situ hybridization method [5], we found that each of 15 transcribed genes was localized as predicted by their chromosomal position and by the known polarized organization of the chromosomes. We also found that, within their specific apical-basal plane, most nascent transcript foci could occupy any radial position. There was no correlation between the apical-basal position of the transcribed locus and the final cytoplasmic site of localization of the RNA along the apical-basal axis of the cell. There was also no relationship between the distance of loci from the nuclear periphery and the amount of nascent mRNA decorating the gene. Our results are consistent with the view that effective transcription can occur without major re-localization of the genes themselves.

Evaluation of recombinant sporozoite antigen SPAG-1 as a vaccine candidate against Theileria annulata by the use of different delivery systems.

The major sporozoite surface antigen of Theileria annulata (SPAG-1) is a candidate for inclusion in a subunit vaccine. In this paper we summarize the results of 4 vaccination experiments using recombinant SPAG-1 expressed in different systems and presented in different adjuvants. The antigen has been presented as either a C terminal 108 amino acid peptide (called SR1) expressed as both beta-galactosidase and hepatitis B core antigen fusions or as a full-length form expressed as a GST fusion with an N terminal His6 tag. We used different adjuvants, namely Freund's, saponin, ISCOMs and a proprietary adjuvant supplied by SmithKline Beecham, which we call SKBA. The data point to the conclusion that SPAG-1 can elicit partial protection and is therefore suitable for inclusion in an eventual multicomponent subunit vaccine.

Mechanism(s) of attenuation of Theileria annulata vaccine cell lines.

Attenuated vaccines are an important means of controlling Theileria annulata infection of cattle. Production is by prolonged cultivation of macroschizont-infected cells. The mechanism of attenuation remains unclear. There are three general nonmutually exclusive possibilities: Selection of avirulent subpopulations, genome rearrangements and alterations in gene expression. Several groups, including ours, have provided evidence that the population structure usually tends to simplify during attenuation. Our data on the T. annulata (Ta) Ankara cell line show that attenuation is not necessarily accompanied by the population becoming clonal. We have been unable to detect large DNA rearrangements. Evidence for alterations in host and parasite gene expression during attenuation is available. With respect to the host we have shown that attenuation is accompanied by loss of expression of parasite induced matrix metalloproteinases (MMPs). However, in different lines different protease activities are involved. In the T. annulata Ode line we have shown that 8 activities (including MMP9) are downregulated and that this correlates with a loss of metastatic behaviour. This has previously been shown in vitro using reconstituted basement membrane (Matrigel) and is demonstrated in vivo using scid mice in this study. Thus part of the pathology, namely the ability to disseminate, mediated by host MMPs, is lost upon attenuation. Re-isolation experiments have shown that the reduction/loss of MMP is a stable transferable trait. A logical extension is that loss of MMP activity (and virulence in general) must be at the most fundamental level a genetic trait of the parasite. Evidence for loss of parasite gene expression is implied by the loss of the ability to differentiate into merozoites on attenuation. Specific evidence for loss of parasite gene expression has been obtained using differential RNA display. We view virulence as a multifactorial phenomenon involving interacting subpopulations of cells and attenuation is a threshold effect whereby the number of virulence factors is reduced below a critical level. On this basis there will be many different ways to achieve attenuation.

Infectivity and cross-immunity studies of Theileria lestoquardi and Theileria annulata in sheep and cattle: II. In vitro studies.

In the studies previously reported, the tick-borne protozoan parasites Theileria lestoquardi and Theileria annulata were shown to differ in their capacity to infect sheep and cattle. In the studies presented here, these findings were further supported. In vitro infectivity of T. lestoquardi and T. annulata sporozoites for peripheral blood mononuclear cells of sheep and cattle were determined by analysis of cell cultures for cell proliferation, the detection of parasites in Giemsa-stained cytospin smears and the establishment of continuously growing schizont-infected cell lines. In the same way, the development of schizont-infected cells into continuously growing cell lines was studied with material isolated ex vivo from the sheep and cattle undergoing primary infections described elsewhere. Comparisons were also made between development of ex vivo cell lines from animals undergoing primary infections with those of the animals undergoing challenge infection with the other parasite species. Theileria species specific primers were used in a PCR to determine the identity of the parasites in the cell lines. These in vitro studies confirmed earlier observations that T. lestoquardi was unable to infect cattle, whereas infection of all sheep with T. annulata was proven. Moreover, earlier indications of the development of partial cross-immunity in sheep of T. annulata to T. lestoquardi and vice versa were strengthened. These findings may thus have consequences for the understanding of the epidemiology of T. lestoquardi infections of sheep. On the other hand. since piroplasms were not demonstrated in sheep infected with T. annulata, such sheep will not be infective to ticks and will consequently be unlikely to play a role in the maintenance and transmission of T. annulata to cattle.

Stage-specific activity in vitro on the Theileria infection process of serum from calves treated prophylactically with buparvaquone.

An in vitro method for testing activity of buparvaquone in serum on the infection and development of Theileria in its bovine host mononuclear cells is described and results compared with the effect exhibited in vivo. Serum samples were collected over a time course from calves in a clinical trial of 5 mg kg(-1) buparvaquone prophylaxis on Theileria annulata or T. parva experimental infection. To evaluate drug levels and persistence in each animal for a period of 14 days and its effect on the early infection stages, the sera were tested on established macroschizont infected cell lines and against the in vitro infection and development process of the sporozoite and trophozoite stages of the two Theileria species. Results from the in vitro assays show that buparvaquone in serum can completely prevent the establishment of Theileria infection during the first 48 h after administration at 5 mg kg(-1). After seven days, levels are sufficient to delay the establishment of infection. The drug is more effective in the prevention of the de novo development of the parasite in cells than against established macroschizont infected cell culture. At low concentrations, it is more effective against T. parva than against T. annulata. Drug effect peaks during the first 24 h but residual effect persists for 14 days, particularly against T. parva infection. These novel findings demonstrate how high doses of buparvaquone could over-protect calves if used in the 'infection-and-treatment' method of immunisation when drug is administered prophylactically at the same time as infection with live sporozoites. It is suggested that in certain high Theileria risk situations there may be potential for the immunoprophylactic use of buparvaquone without simultaneous infection. The in vitro assay itself has been shown to be of value as a model for Theileria establishment in cattle.