Vaccine or field strains: the jigsaw pattern of infectious bronchitis virus molecular epidemiology in Poland

Infectious bronchitis (IB), caused by infectious bronchitis virus (IBV), account for severe economic losses in the poultry industry. The continuous emergence of a multitude of IBV variants poses many challenges for its diagnosis and control, and live attenuated vaccines, despite their routine use, still plays a significant role in driving IBV evolution, further complicating the epidemiological scenario. Unfortunately, the impact of different vaccination strategies on IB control, epidemiology, and diagnosis has rarely been investigated. This work presents the results of a large-scale diagnostic survey performed in Poland to study IBV molecular epidemiology and how vaccination may affect the viral circulation in the field. To this purpose, 589 samples were collected between May 2017 and January 2019, tested by reverse transcription-PCR for IBV and sequenced. Vaccine and field strains were discriminated based on genetic and anamnestic information. The most commonly detected lineages were 793B (79%) and variant 2 (17.4%), with sporadic detections of QX, Mass, and D274-like strains. Most of the detected strains had a vaccine origin: 46.3% matched one of the applied vaccines, while 36.5% were genetically related to vaccines not implemented in the respective protocol. Besides their practical value for the proper planning of vaccination protocols in Poland, these results suggest that only a fraction (17.2%) of the circulating strains are field ones, imposing a careful assessment of the actual IBV field menaces. Moreover, phenomena like vaccine spreading and persistence seem to occur commonly, stressing the need to further study the epidemiological consequences of the extensive use of live vaccines

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.info:eu-repo/semantics/acceptedVersio

Vaccine or field strains: the jigsaw pattern of infectious bronchitis virus molecular epidemiology in Poland

Infectious bronchitis (IB), caused by infectious bronchitis virus (IBV), account for severe economic losses in the poultry industry. The continuous emergence of a multitude of IBV variants poses many challenges for its diagnosis and control, and live attenuated vaccines, despite their routine use, still plays a significant role in driving IBV evolution, further complicating the epidemiological scenario. Unfortunately, the impact of different vaccination strategies on IB control, epidemiology, and diagnosis has rarely been investigated. This work presents the results of a large-scale diagnostic survey performed in Poland to study IBV molecular epidemiology and how vaccination may affect the viral circulation in the field. To this purpose, 589 samples were collected between May 2017 and January 2019, tested by reverse transcription-PCR for IBV and sequenced. Vaccine and field strains were discriminated based on genetic and anamnestic information. The most commonly detected lineages were 793B (79%) and variant 2 (17.4%), with sporadic detections of QX, Mass, and D274-like strains. Most of the detected strains had a vaccine origin: 46.3% matched one of the applied vaccines, while 36.5% were genetically related to vaccines not implemented in the respective protocol. Besides their practical value for the proper planning of vaccination protocols in Poland, these results suggest that only a fraction (17.2%) of the circulating strains are field ones, imposing a careful assessment of the actual IBV field menaces. Moreover, phenomena like vaccine spreading and persistence seem to occur commonly, stressing the need to further study the epidemiological consequences of the extensive use of live vaccines

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 dif- ferent 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 identi- fication even in challenging field conditions or in poor conservation of the samples; moreover, the first mor- phological description of C. boopis larvae is provided

Porcine circovirus 2 (PCV-2) genetic variability under natural infection scenario reveals a complex network of viral quasispecies

Porcine circovirus 2 (PCV-2) is a virus characterized by a high evolutionary rate, promoting the potential emergence of different genotypes and strains. Despite the likely relevance in the emergence of new PCV-2 variants, the subtle evolutionary patterns of PCV-2 at the individual-host level or over short transmission chains are still largely unknown. This study aimed to analyze the within-host genetic variability of PCV-2 subpopulations to unravel the forces driving PCV-2 evolution. A longitudinal weekly sampling was conducted on individual animals located in three farms after the first PCV-2 detection. The analysis of polymorphisms evaluated throughout the full PCV-2 genome demonstrated the presence of several single nucleotide polymorphisms (SNPs) especially in the genome region encoding for the capsid gene. The global haplotype reconstruction allowed inferring the virus transmission network over time, suggesting a relevant within-farm circulation. Evidences of co-infection and recombination involving multiple PCV-2 genotypes were found after mixing with pigs originating from other sources. The present study demonstrates the remarkable within-host genetic variability of PCV-2 quasispecies, suggesting the role of the natural selection induced by the host immune response in driving PCV-2 evolution. Moreover, the effect of pig management in multiple genotype coinfections occurrence and recombination likelihood was demonstrated

Hydrogen induced optically-active defects in silicon photonic nanocavities

This work was supported by Era-NET NanoSci LECSIN project coordinated by F. Priolo, by the Italian Ministry of University and Research, FIRB contract No. RBAP06L4S5 and by the EPSRC UKSp project. Partial financial support by the Norwegian Research Council is also acknowledged.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.Publisher PDFPeer reviewe

Is medical device regulatory compliance growing as fast as extended reality to avoid misunderstandings in the future?

Purpose: European Extended Reality (XR) industry is expected to significantly increase by 2025 with an extreme impact on the Healthcare scenario. Considering that the transition period for the Medical Device Regulation 2017/745 (MDR 2017/745) will end in May 2024, purpose of this study is to assess whether the Medical Device Regulatory Compliance is ready to cope with the inclusion of XR and its possible social and economic impact in the world of medical device software (MDSW). Methods: XR publications patterns were evaluated since MDR 2017/745 release on different databases. European normative about MDSW are consulted, followed by the European Database of Medical Devices (EUDAMED). Results: The number of publications on XR have increased since 2017 and healthcare is the third highest-impacted subject area. Specific classes for software have been introduces in the European Nomenclature of Medical Devices (EMDN) and some XR applications have already been registered in EUDAMED classified as MDSW. Conclusions: XR will become intrinsic in everyday medical protocol and guidelines. The establishment of the IEEE Virtual Reality and Augmented Reality Working Group and the statement of VR for remoting surgery as a MDSW in MDCG 2019-11 are demonstration of the necessity of MD regulatory compliance in being able to keep up with the upcoming XR technologies. The Authors agree that the competent authorities should consider intervening in the European Regulative Compliance to cope with the revolution of Phygital in Healthcare and to regulate procedures involving the use of XR in medicine preventing future misunderstanding and criticalities especially for high risk situations

A Frailty Index based on clinical data to quantify mortality risk in dogs

Frailty is defined as a decline in an organism's physiological reserves resulting in increased vulnerability to stressors. In humans, a single continuous variable, the so-called Frailty Index (FI), can be obtained by multidimensionally assessing the biological complexity of an ageing organism. Here, we evaluate this variability in dogs and compare it to the data available for humans. In dogs, there was a moderate correlation between age and the FI, and the distribution of the FI increased with age. Deficit accumulation was strongly related to mortality. The effect of age, when combined with the FI, was negligible. No sex-related differences were evident. The FI could be considered in epidemiological studies and/or experimental trials to account for the potential confounding effects of the health status of individual dogs. The age-related deficit accumulation reported in dogs is similar to that demonstrated in humans. Therefore, dogs might represent an excellent model for human aging studies

Approaching the seismogenic source of the Calabria 8 September 1905 earthquake: New geophysical, geological and biochemical data from the S. Eufemia Gulf (S Italy)

Recognizing the seismogenic source of major historical earthquakes, particularly when these have occurred offshore, is a long-standing issue across the Mediterranean Sea and elsewhere. The destructive earthquake (M ~7) that struck western Calabria (southern Italy) on the night of 8 September 1905 is one such case. having various authors proposed a seismogenic source, with apparently diverse hypotheses and without achieving a unique solution. To gain novel insight into the crustal volume where the 1905 earthquake took place and to seek a more robust solution for the seismogenic source associated with this destructive event, we carried out a well-targeted multidisciplinary survey within the Gulf of S. Eufemia (SE Tyrrhenian Sea), collecting geophysical data, oceanographic measurements, and biological, chemical and sedimentary samples. We identified three main tectonic features affecting the sedimentary basin in the Gulf of S. Eufemia: 1) a NE-SW striking, ca. 13-km-long, normal fault, here named S. Eufemia Fault; 2) a WNW-striking polyphased fault system; and 3) a likely E-W trending lineament. Among these, the normal fault shows evidence of activity witnessed by the deformed recent sediments and by its seabed rupture along which, locally, fluid leakage occurs. Features in agreement with the anomalous distribution of prokaryotic abundance and biopolymeric C content, resulted from the shallow sediments analyses. The numerous seismogenic sources proposed in the literature during the past 15 years make up a composite framework of this sector of western Calabria, that we tested against a) the geological evidence from the newly acquired dataset, and b) the regional seismotectonic models. Such assessment allows us to propose the NE-SW striking normal fault as the most probable candidate for the seismogenic source of the 1905 earthquake. Re-appraising a major historical earthquake as the 1905 one enhances the seismotectonic picture of western Calabria. Further understanding of the region and better constraining the location of the seismogenic source may be attained through integrated interpretation of our data together with a) on-land field evidence, and b) seismological modeling

Canine parvovirus (CPV) phylogeny is associated with disease severity

After its first identification in 1978, canine parvovirus (CPV) has been recognized all around the world as a major threat for canine population health. This ssDNA virus is characterized by a high substitution rate and several genetic and phenotypic variants emerged over time. Overall, the definition of 3 main antigenic variants was established based on specific amino acid markers located in a precise capsid position. However, the detection of several minor variants and incongruence observed between the antigenic classification and phylogeny have posed doubts on the reliability of this scheme. At the same time, CPV heterogeneity has favored the hypothesis of a differential virulence among variants, although no robust and consistent demonstration has been provided yet. The present study rejects the antigenic variant concept and attempts to evaluate the association between CPV strain phylogeny, reconstructed using the whole information contained in the VP2 coding gene, and several clinical and hemato-biochemical parameters, assessed from 34 CPV infected dogs at admission. By using different statistical approaches, the results of the present study show an association between viral phylogeny and host parameters ascribable to immune system, coagulation profile, acute phase response and, more generally, to the overall picture of the animal response. Particularly, a strong and significant phylogenetic signal was proven for neutrophil count and WBC. Therefore, despite the limited sample size, a relation between viral phylogeny and disease severity has been observed for the first time, suggesting that CPV virulence is an inherited trait. The likely existence of clades with different virulence highlights once more the relevance of intensive epidemiological monitoring and research on CPV evolution to better understand the virulence determinants, their epidemiology and develop adequate countermeasures