Neutralising antibodies to West Nile virus detected in horses in Windhoek, Namibia.

ABSTRACT: West Nile virus (WNV) is a vector-borne virus maintained in nature by a bird-mosquito cycle. However, it can occasionally and accidentally infect horses and human beings, leading to sometimes severe or even fatal outcomes in these species. Therefore, the monitoring of its circulation and disease occurrence is of relevance. Unfortunately, it is underdiagnosed or not diagnosed in several African counties, including Namibia, where no data is currently available for horses. In this study, 98 horses in three different stables in the Windhoek city area were investigated. They were found to have a seroprevalence of approximately 7%. Positive reactions were seen at all three stables, suggesting a greater than expected prevalence of the virus. This is the first report of serological evidence for the presence of the virus in horses in Nambia. Even though clinical signs were not reported in any of the stables from which the sera were derived, the seroprevalence to the virus suggests that horses with high genetic and/or economic value could benefit from vaccination against WNV. Because of the zoonotic potential of the virus, these findings are also of significance to human health authorities.

First detection of porcine circovirus type 2e in Europe.

Porcine circovirus 2 (PCV-2) infections are among the most economically important in swine farming. Because of the high evolutionary rate of PCV-2, several variants have emerged and are currently classified into several genotypes. However, only three (i.e. PCV-2a, PCV-2b, and PCV-2d) have a worldwide distribution, with other genotypes restricted to certain geographical regions and/or for limited time periods. Underdiagnosis or underreporting of these genotypes cannot be excluded. This is the first report of the detection and genetic characterisation of the PCV-2e genotype in Europe, from sows on a farm in Italy showing no clinical evidence of porcine circovirus disease. A follow-up study demonstrated persistent subclinical evidence of PCV-2e on the farm, at low frequency and viral load. This incidental finding emphasises the need for more intensive routine monitoring activities involving asymptomatic animals, coupled with DNA sequencing and data sharing. Considering the relevant genetic and phenotypic divergence of such genotypes, the actual efficacy of currently applied vaccines and diagnostic assays should be further evaluated.

Free carrier enhanced depletion in ZnO nanorods decorated with bimetallic AuPt nanoclusters.

The decoration of semiconductor nanostructures with small metallic clusters usually leads to an improvement of their properties in sensing or catalysis. Bimetallic cluster decoration typically is claimed to be even more effective. Here, we report a detailed investigation of the effects of Au, Pt or AuPt nanocluster decoration of ZnO nanorods on charge transport, photoluminescence and UV sensitivity. ZnO nanorods were synthesized by chemical bath deposition while decoration with small nanoclusters (2-3 nm in size) was achieved by a laser-ablation based cluster beam deposition technology. The structural properties were investigated by scanning electron microscopy, high resolution transmission electron microscopy, X-ray photoelectron spectroscopy and Rutherford backscattering spectrometry, and the optoelectronic properties by current-voltage and photoluminescence measurements. The extent of band bending at the cluster-ZnO interface was quantitatively modeled through numerical simulations. The decoration of ZnO nanorods with monometallic Au or Pt nanoclusters causes a significant depletion of free electrons below the surface, leading to a reduction of UV photoluminescence, an increase of ZnO nanorod dark resistance (up to 200 times) and, as a consequence, an improved sensitivity (up to 6 times) to UV light. These effects are strongly enhanced (up to 450 and 10 times, respectively) when ZnO nanorods are decorated with bimetallic AuPt nanoclusters that substantially augment the depletion of free carriers likely due to a more efficient absorption of the gas molecules on the surface of the bimetallic AuPt nanoclusters than on that of their monometallic counterparts. The depletion of free carriers in cluster decorated ZnO nanorods is quantitatively investigated and modelled, allowing the application of these composite materials in UV sensing and light induced catalysis.

Diagnostic accuracy of two DNA-based molecular assays for detection of porcine circovirus 3 in swine population using Bayesian latent class analysis.

Molecular-based tools sometimes are the only laboratory techniques available to detect a recently discovered agent, and their validation without the existence of previously described 'gold standard' methods poses a challenge for the diagnosticians. A good example within this scenario is the recently described porcine circovirus 3 (PCV-3) in the swine population worldwide, from which only few PCR methods have been described. Therefore, the primary objective of this study was to estimate the diagnostic accuracy of a direct PCR (dPCR) and a real-time qPCR (qPCR) for detection of PCV-3 in Italian swine population. Bayesian latent class analysis approach was used to rigorously assess their features and applicability in routine diagnostic activity. Data on dPCR and qPCR were available from 116 domestic pigs, which were randomly selected from 55 farms located at different regions in Northern Italy. The sensitivity (Se) estimates of dPCR (94%; posterior credible interval (PCI%) 84-100) and qPCR (96%; PCI% 90-100) were high and similar. The estimated specificity (Sp) of both dPCR and qPCR assays was around 97%. dPCR and qPCR assays showed a high and comparable Se and Sp estimates for the detection of PCV-3 in Italian swine population. SIGNIFICANCE AND IMPACT OF THE STUDY: The continuous discovery of new pathogens poses a challenge in the development and evaluation of adequate diagnostic tools. In fact, since molecular-based tools sometimes are the only available laboratory techniques, it is typically difficult to evaluate their diagnostic performances in the absence of a gold standard. The present study assesses this issue, demonstrating the excellent performances of two PCR-based assays for porcine circovirus 3 (PCV-3) detection using a Bayesian latent class analysis approach. Therefore, the molecular tests evaluated under this study constitute reliable tools for the routine diagnosis and surveillance programs of PCV-3 circulating in swine populations.

Morphological and molecular characterization of adults and larvae of Crassicauda spp. (Nematoda: Spirurida) from Mediterranean fin whales Balaenoptera physalus (Linnaeus, 1758).

Crassicauda boopis is known to infect the kidneys and vascular system of mysticetes included Balaenoptera physalus and has been recently reported in Mediterranean waters. Identification at the species level relies on the observation of morphological features of the adult parasites, but field conditions during necropsy and the massive reaction of the host's immune system often prevent optimal conservation of the extremities. Moreover, larval stages of Crassicauda have never been described and no sequences are available in public databases to help such identification. Adult and larvae of Crassicauda were isolated from four specimens of B. physalus and studied with morphological and molecular techniques. Specimens of C. anthonyi, C. grampicola and Crassicauda sp. isolated from Ziphius cavirostris, Grampus griseus, Stenella coeruleoalba and Tursiops truncatus respectively were studied as well. Sequences of nuclear markers 18S and ITS-2 and of mitochondrial gene cox1 were obtained and phylogenetic relationships within the genus Crassicauda were analysed. Analysis of the ITS2 grouped the different species in accordance with morphological identification, as already evidenced in literature for other Spirurida. A higher intra-specific variability was observed for the cox1 gene, for which two species (C. grampicola and C. anthonyi) did not appear as monophyletic in the tree. Well-developed non-attached larval specimens in the intestinal lumen of a whale calf were molecularly identified as C. boopis, allowing new insights on the life cycle of this species. This work broadens the genetic database on cetaceans parasites, allowing species identification even in challenging field conditions or in poor conservation of the samples; moreover, the first morphological description of C. boopis larvae is provided.

Phylogeny and evolution of infectious bursal disease virus circulating in Turkish broiler flocks.

The emergence of new infectious bursal disease virus (IBDV) variants can threaten poultry health and production all over the world causing significant economic losses. Therefore, this study was performed to determine IBDV molecular epidemilogy, VP2 gene variation, and corresponding pathological lesions in IBDV infected chickens in Turkey. For this, 1855 bursa of Fabricius samples were collected from 371 vaccinated broiler flocks. Atrophia and haemorrhages were seen in the bursa Fabricius of very virulent IBDV (vvIBDV) infected chickens. Partial VP2 gene was sequenced and phylogenetic, recombination, and evolutionary analyses were performed. 1548 (83.5%) out of 1855 of bursa of Fabricius samples were IBDV positive and 1525 of those could be sequenced. The recombination analysis did not detect occurrence of any recombination event among the Turkish strains. Among 1525 sequenced samples, 1380 of them were found to be classical strains. Among 1380 classical strains, 1317 were similar to IBDV 2512, 11 to Faragher 52/70, 40 to 228 E, and 12 to Lukert strain. Out of 1525 reverse transcriptase ploymerase chain reaction positive samples, 144 of them were found to be similar to vvIBDV-VP2 gene reported to GenBank previously. The phylogenetic tree performed on a broad sequence dataset demonstrated grouping of vvIBDV Turkish strains in three different clusters, including sequences collected also from Iraq and Kuwait (Cluster 1), Indian (Cluster 2), and a distinct Turkish-only cluster (Cluster 3). The evolutionary rate estimation on branches/clades including Turkish strain mirrored the expected one for RNA viruses and no significant differences were found among different considered branches. In conclusion, results of this study indicate that vvIBDV strains similar to those circulating in various countries in the Middle East are present and undergoing evolution in chickens from Turkish broiler flocks. This point needs to be taken into account in planning adequate control strategies.

Photoluminescence Study of the Influence of Additive Ammonium Hydroxide in Hydrothermally Grown ZnO Nanowires.

We report the influence of ammonium hydroxide (NH4OH), as growth additive, on zinc oxide nanomaterial through the optical response obtained by photoluminescence (PL). A low-temperature hydrothermal process is employed for the growth of ZnO nanowires (NWs) on seedless Au surface. A more than two order of magnitude change in ZnO NW density is demonstrated via careful addition of NH4OH in the growth solution. Further, we show by systematic experimental study and PL characterization data that the addition of NH4OH can degrade the optical response of ZnO NWs produced. The increase of growth solution basicity with the addition of NH4OH may slowly degrade the optical response of NWs by slowly etching its surfaces, increasing the point defects in ZnO NWs. The present study demonstrates the importance of growth nutrients to obtain quality controlled density tunable ZnO NWs on seedless conducting substrates.

Retrospective detection of Porcine circovirus 3 (PCV-3) in pig serum samples from Spain.

Porcine circovirus 3 (PCV-3) is an emerging circovirus species that has recently been reported in different countries around the world, suggesting a widespread circulation. In this study, sera samples originating from 654 pigs of different production phases and clinical/pathological conditions, submitted for diagnostic purposes between 1996 and 2017, were randomly selected. Detection of PCV-3 genome in such samples was attempted with a previously described PCR method, and the partial genome sequence was obtained from selected PCV-3-positive samples from different years. Compiled data confirmed that PCV-3 has been circulating in the Spanish pig population since 1996. The overall frequency of PCV-3 PCR-positive samples in the study period was 11.47% (75 of 654). Phylogenetic analysis of twelve PCV-3 partial sequences obtained showed a high nucleotide identity with the already known PCV-3 sequences, with minor variations among years. No significant correlation was found between the detection of PCV-3 and any production phase nor clinical/pathological condition. These results confirm PCV-3 circulation at least since 1996 in the Spanish pig population with a low/moderate frequency. Although the information obtained was limited, PCV-3 did not appear to be linked to any specific pathological condition or age group.

Full-genome sequencing of porcine circovirus 3 field strains from Denmark, Italy and Spain demonstrates a high within-Europe genetic heterogeneity.

Porcine circovirus 3 (PCV3) is a new species of the Circovirus genus, which has recently been associated with different clinical syndromes. Its presence has been reported in different countries of North and South America, Asia and recently also Europe (Poland). However, different from the other continents, no European PCV3 sequence is currently available in public databases. There is a strong need of epidemiological data and full-genome sequences from Europe because of its relevance in the understanding of PCV3 molecular epidemiology and control. To fill this lack of information, samples collected in Denmark, Italy and Spain in 2016 and 2017 were screened for PCV3. Of the Danish samples, 36 of 38 the lymph nodes, six of 20 serum samples and two of 20 lung samples tested positive. Similarly, 10 of 29 lungs, 20 of 29 organ pools, six of 33 sera and one of eight nasal swabs tested PCV3 positive in Italy. Fourteen of 94 serum pools from seven of 14 Spanish farms were also positive. Despite the convenience nature of the sampling prevents any precise prevalence estimation, the preliminary screening of the data from three European countries confirmed a rather wide PCV3 distribution in Europe. Furthermore, the analysis of the six obtained complete European PCV3 genomes and their comparison with the public available sequences seems to support a remarkable worldwide PCV3 circulation. These results underline once more the urgency of more extensive epidemiological studies to refine the current knowledge on PCV3 evolution, transmission, spreading patterns and impact on pig health.

Evaluation of 793/B-like and Mass-like vaccine strain kinetics in experimental and field conditions by real-time RT-PCR quantification.

Infectious bronchitis virus (IBV) is a great economic burden both for productive losses and costs of the control strategies. Many different vaccination protocols are applied in the same region and even in consecutive cycles on the same farm in order to find the perfect balance between costs and benefits. In Northern Italy, the usual second vaccination is more and more often moved up to the chick's first d of life. The second strain administration together with the common Mass priming by spray at the hatchery allows saving money and time and reducing animal stress. The present work compared the different vaccine strains (Mass-like or B48, and 1/96) kinetics both in field conditions and in a 21-day-long experimental trial in broilers, monitoring the viral replication by upper respiratory tract swabbing and vaccine specific real time reverse transcription PCR (RT-PCR) quantification. In both field and experimental conditions, titers for all the vaccines showed an increasing trend in the first 2 wk and then a decrease, though still remaining detectable during the whole monitored period. IBV field strain and avian Metapneumovirus (aMPV) presence also was also investigated by RT-PCR and sequencing, and by multiplex real-time RT-PCR, respectively, revealing a consistency in the pathogen introduction timing at around 30 d, in correspondence with the vaccine titer's main decrease. These findings suggest the need for an accurate knowledge of live vaccine kinetics, whose replication can compete with the other pathogen one, providing additional protection to be added to what is conferred by the adaptive immune response.

First Molecular Characterization of Avian Metapneumovirus (aMPV) in Turkish Broiler Flocks.

Viral respiratory diseases, including avian metapneumovirus (aMPV), have a significant economic impact on poultry industries. The frequency and genotype diversity of aMPV in Turkish broiler flocks is not known at present. The aim of this study was to report the first molecular identification and phylogeny of aMPV, which is circulating in Turkish broiler flocks. Trachea tissue samples and tracheal swabs were collected from 110 broiler flocks distributed in different geographical regions in Turkey between March 2017 and March 2018. Detection of aMPV was confirmed with the use of universal reverse transcriptase (RT) PCR, and eight (7.2%) broiler farms were positive for aMPV. Sequence analysis of the G gene revealed the exclusive presence of subtype B viruses. Three field isolates clustered closely with a 2002 Israel isolate, indicating a potential transmission route between these two countries and through the Middle East. The remaining five field isolates were closely related to a vaccine strain, even though broiler flocks in Turkey are not routinely vaccinated against aMPV. Therefore, we speculate these five isolates could have originated from nearby vaccinated turkey farms. Additionally, the presence of some nucleotide substitutions compared to the reference vaccine sequence suggests prolonged circulation and evolution of the original vaccine virus or a vaccine subpopulation was selected under field conditions. This evidence emphasizes the need for further detailed and more systemic approaches to evaluate aMPV spread and evolution in order to design effective control strategies.

Nota de investigación- Primera caracterización molecular de metapneumovirus aviar (aMPV) en parvadas de pollo de engorde en Turquía. Las enfermedades respiratorias virales, incluido el metapneumovirus aviar (aMPV), tienen un impacto económico significativo en la industrias avícola. La diversidad de la frecuencia y el genotipo de aMPV en las parvadas de pollos de engorde en Turquía no se conocen en la actualidad. El objetivo de este estudio fue reportar la primera identificación molecular y la filogenia de un metapneumovirus aviar, que circula en parvadas de pollos de engorde turcos. Se recolectaron muestras de tejido de tráquea e hisopos traqueales de 110 parvadas de pollos de engorde distribuidas en diferentes regiones geográficas de Turquía entre marzo del 2017 y marzo del 2018. La detección de metapneumovirus aviar se confirmó con el uso de un método de universal transcriptasa reversa y PCR. Ocho (7.2%) granjas de pollos de engorde fueron positivas para metapneumovirus aviar. El análisis de secuencia del gene G reveló la presencia exclusiva de virus de subtipo B. Tres virus de campo se agruparon estrechamente con un metapneumovirus de Israel del año 2002, lo que indica una posible ruta de transmisión entre estos los dos países y el Medio Oriente. Los cinco metapneumovirus de campo restantes estaban estrechamente relacionados con una cepa de vacuna, a pesar de que las parvadas de pollos de engorde en Turquía no se vacunan rutinariamente contra metapneumovirus aviar. Por lo tanto, se especula que estos cinco metapneumovirus podrían haberse originado en granjas cercanas con pavos vacunados. Además, la presencia de algunas sustituciones de nucleótidos en comparación con la secuencia de la vacuna de referencia sugiere una circulación prolongada y la evolución del virus de la vacuna original o una subpoblación de la vacuna se seleccionó en condiciones de campo. Esta evidencia enfatiza la necesidad de enfoques más detallados y más sistémicos para evaluar la propagación y evolución de metapneumovirus aviar a fin de diseñar estrategias de control efectivas. Abbreviations: aMPV = avian metapneumovirus; cDNA = complementary DNA; F = fusion; G = attachment; RT-PCR = reverse-transcriptase PCR.

Genome sequence analysis of a distinctive Italian infectious bursal disease virus.

In a recent study, an emerging infectious bursal disease virus (IBDV) genotype (ITA) was detected in IBDV-live vaccinated broilers without clinical signs of infectious bursal disease (IBD). VP2 sequence analysis showed that strains of the ITA genotype clustered separately from vaccine strains and from other IBDV reference strains, either classic or very virulent. In order to obtain a more exhaustive molecular characterization of the IBDV ITA genotype and speculate on its origin, genome sequencing of the field isolate IBDV/Italy/1829/2011, previously assigned to the ITA genotype, was performed, and the sequences obtained were compared to the currently available corresponding sequences. In addition, phylogenetic and recombination analyses were performed. Interestingly, multiple amino acid (AA) sequence alignments revealed that the IBDV/Italy/1829/2011 strain shared several AA residues with very virulent IBDV strains as well as some virulence markers, especially in the VP1 protein. Nevertheless, sequence analysis demonstrated the presence of several residues typical of IBDV strains at a low degree of virulence in the IBDV/Italy/1829/2011 strain. Although homologous recombination and reassortant phenomena may occur naturally among different IBDV strains, no evidence of those events was found in the genome of the IBDV/Italy/1829/2011 strain, which was confirmed to be a genetically distinctive IBDV genotype.

A novel variant of the infectious bronchitis virus resulting from recombination events in Italy and Spain.

Infectious bronchitis is considered to be one of the most devastating diseases in poultry. Control of its spread is typically attempted through biosecurity measures and extensive vaccination. However, the remarkable genetic and antigenic variability of the virus, which originate from both mutations and recombination events, represents an unsolved challenge for this disease. The present study reports on the emergence and spread of recombinant clusters detected in Italy and Spain between 2012 and 2014. A total of 36 Spanish and Italian infectious bronchitis virus (IBV) field strains were investigated and genetically characterized using phylogenetic, molecular, recombination and selection pressure analyses of the complete S1 gene. Based on the partial S1 sequencing, 27 IBV strains originating from Spain and nine from Italy were initially classified as being closely related to the Guandong/Xindadi (XDN) genotype. Phylogenetic analysis of the complete S1 gene revealed that the XDN strains formed a homogeneous clade with the Spanish IBV isolates within the QX genotype, whereas there was higher variability within the Italian strains. Recombination analysis determined that these strains belonged to four groups, which originated from independent recombination events between the QX and 793B IBV genotypes. Our data support the hypothesis of two different scenarios: firstly, in Spain, the large and homogeneous clade probably originated from a single offspring of the recombinant founder, which became dominant and spread throughout the country. Secondly, the nine Italian recombinants, which are characterized by three different recombination patterns, probably represent less fitted strains, because they were less viable with respect to their recombinant parents.

Gamma and Deltacoronaviruses in quail and pheasants from Northern Italy1.

In view of the restricted knowledge on the diversity of coronaviruses in poultry other than chicken, this study aimed to investigate the genetic diversity of coronaviruses in quail, pheasant, and partridge from two regions of Northern Italy. To this end, pools of tracheal and cloacal swabs from European quail (Coturnix Coturnix) and intestinal tract from pheasants (Phasianus Colchicus) and partridge (Perdix Perdix) flocks, with or without enteric signs, were collected during 2015. Avian coronavirus (Gammacoronavirus) was detected in quail not vaccinated against Infectious Bronchitis Virus (IBV) and in pheasants vaccinated with an IBV Massachusetts serotype. Based on DNA sequences for the gene encoding the S protein, the avian coronaviruses detected in the quail and pheasant are related to the IBV 793B and Massachusetts types, respectively. However, RNA-dependent RNA polymerase (RdRp) analyses showed the susceptibility of quail also to Deltacoronaviruses, suggesting that quail and pheasant avian coronaviruses share spike genes identical to chicken IBV spike genes and quail might host Deltacoronavirus.

Radiative mechanism and surface modification of four visible deep level defect states in ZnO nanorods.

Visible luminescence from ZnO nanorods (NRs) is attracting large scientific interest for light emission and sensing applications. We study visible luminescent defects in ZnO NRs as a function of post growth thermal treatments, and find four distinct visible deep level defect states (VDLSs): blue (2.52 eV), green (2.23 eV), orange (2.03 eV), and red (1.92 eV). Photoluminescence (PL) studies reveal a distinct modification in the UV (3.25 eV) emission intensity and a shift in the visible spectra after annealing. Annealing at 600 °C in Ar (Ar600) and O2 (O600) causes a blue and red-shift in the visible emission band, respectively. All samples demonstrate orange emission from the core of the NR, with an additional surface related green, blue, and red emission in the As-Prep, Ar600, and O600 samples, respectively. From PL excitation (PLE) measurements we determine the onset energy for population of the various VDLSs, and relate it to the presence of an Urbach tail below the conduction band due to a presence of ionized Zni or Zni complexes. We measured an onset energy of 3.25 eV for the as prepared sample. The onset energy red-shifts in the annealed samples by about 0.05 to 0.1 eV indicating a change in the defect structure, which we relate to the shift in the visible emission. We then used X-ray photoemission spectroscopy (XPS), and elastic recoil detection analysis (ERDA) to understand changes in the surface structure, and H content, respectively. The results of the XPS and ERDA analysis explain how the chemical states are modified due to annealing. We summarize our results by correlating our VDLSs with specific intrinsic defect states to build a model for PL emission in ZnO NRs. These results are important for understanding how to control defect related visible emission for sensing and electroluminescence applications.

Subpopulations in aMPV vaccines are unlikely to be the only cause of reversion to virulence.

Avian metapneumovirus (aMPV) infects respiratory and reproductive tracts of domestic poultry, often involving secondary infections, and leads to serious economic losses in most parts of the world. While in general disease is effectively controlled by live vaccines, reversion to virulence of those vaccines has been demonstrated on several occasions. Consensus sequence mutations involved in the process have been identified in more than one instance. In one previous subtype A aMPV candidate vaccine study, small subpopulations were implicated. In the current study, the presence of subpopulations in a subtype B vaccine was investigated by deep sequencing. Of the 19 positions where vaccine (strain VCO3/50) and progenitor (strain VCO3/60616) consensus sequences differed, subpopulations were found to have sequence matching progenitor sequence in 4 positions. However none of these mutations occurred in a virulent revertant of that vaccine, thereby demonstrating that the majority progenitor virus population had not survived the attenuation process, hence was not obviously involved in any return to virulence. However within the vaccine, a single nucleotide variation was found which agreed with consensus sequence of a derived virulent revertant virus, hence this and other undetected, potentially virulent subpopulations, can be involved in reversion. Much deeper sequencing of progenitor, vaccine and revertant may clarify whether problematic virulent subpopulations are present and therefore whether these need to be routinely removed during aMPV vaccine preparation prior to registration and release.

A sensitive, reproducible, and economic real-time reverse transcription PCR detecting avian metapneumovirus subtypes A and B.

Use of real-time PCR is increasing in the diagnosis of infectious disease due to its sensitivity, specificity, and speed of detection. These characteristics make it particularly suited for the diagnosis of viral infections, like avian metapneumovirus (AMPV), for which effective control benefits from continuously updated knowledge of the epidemiological situation. Other real-time reverse transcription (RT)-PCRs have been published based on highly specific fluorescent dye-labeled probes, but they have high initial cost, complex validation, and a marked susceptibility to the genetic variability of their target sequence. With this in mind, we developed and validated a SYBR Green I-based quantitative RT-PCR for the detection of the two most prevalent AMPV subtypes (i.e., subtypes A and B). The assay demonstrated an analytical sensitivity comparable with that of a previously published real-time RT-PCR and the ability to detect RNA equivalent to approximately 0.5 infectious doses for both A and B subtypes. The high efficiency and linearity between viral titer and crossing point displayed for both subtypes make it suited for viral quantification. Optimization of reaction conditions and the implementation of melting curve analysis guaranteed the high specificity of the assay. The stable melting temperature difference between the two subtypes indicated the possibility of subtyping through melting temperature analysis. These characteristics make our assay a sensitive, specific, and rapid tool, enabling contemporaneous detection, quantification, and discrimination of AMPV subtype A and B.

Hydrogen induced optically-active defects in silicon photonic nanocavities.

We demonstrate intense room temperature photoluminescence (PL) from optically active hydrogen- related defects incorporated into crystalline silicon. Hydrogen was incorporated into the device layer of a silicon on insulator (SOI) wafer by two methods: hydrogen plasma treatment and ion implantation. The room temperature PL spectra show two broad PL bands centered at 1300 and 1500 nm wavelengths: the first one relates to implanted defects while the other band mainly relates to the plasma treatment. Structural characterization reveals the presence of nanometric platelets and bubbles and we attribute different features of the emission spectrum to the presence of these different kind of defects. The emission is further enhanced by introducing defects into photonic crystal (PhC) nanocavities. Transmission electron microscopy analyses revealed that the isotropicity of plasma treatment causes the formation of a higher defects density around the whole cavity compared to the ion implantation technique, while ion implantation creates a lower density of defects embedded in the Si layer, resulting in a higher PL enhancement. These results further increase the understanding of the nature of optically active hydrogen defects and their relation with the observed photoluminescence, which will ultimately lead to the development of intense and tunable crystalline silicon light sources at room temperature.

Quantum confinement and electroluminescence in ultrathin silicon nanowires fabricated by a maskless etching technique.

We present a novel approach for the direct synthesis of ultrathin Si nanowires (NWs) exhibiting room temperature light emission. The synthesis is based on a wet etching process assisted by a metal thin film. The thickness-dependent morphology of the metal layer produces uncovered nanometer-size regions which act as precursor sites for NW formation. The process is cheap, fast, maskless and compatible with Si technology. Very dense arrays of long (several micrometers) and small (diameter of 5-9 nm) NWs have been synthesized. An efficient room temperature luminescence, visible with the naked eye, is observed when NWs are optically excited, exhibiting a blue-shift with decreasing NW size in agreement with quantum confinement effects. A prototype device based on Si NWs has been fabricated showing a strong and stable electroluminescence at low voltages. The relevance and the perspectives of the reported results are discussed, opening the route toward novel applications of Si NWs.

Structural and optical properties of silicon nanocrystals grown by plasma-enhanced chemical vapor deposition.

Silicon nanocrystals (Si-nc) embedded in SiO2 matrix have been prepared by high temperature thermal annealing (1000-1250 degrees C) of substoichiometric SiOx films deposited by plasma-enhanced chemical vapor deposition (PECVD). Different techniques have been used to examine the optical and structural properties of Si-nc. Transmission electron microscopy analysis shows the formation of nanocrystals whose sizes are dependent on annealing conditions and deposition parameters. The spectral positions of room temperature photoluminescence are systematically blue shifted with reduction in the size of Si-nc obtained by decreasing the annealing temperature or the Si content during the PECVD deposition. A similar trend has been found in optical absorption measurements. X-ray absorption fine structure measurements indicate the presence of an intermediate region between the Si-nc and the SiO2 matrix that participates in the light emission process. Theoretical observations reported here support these findings. All these efforts allow us to study the link between dimensionality, optical properties, and the local environment of Si-nc and the surrounding SiO2 matrix.