Search

Equine hepacivirus (EqHV, Flaviviridae, hepacivirus) is a small, enveloped RNA virus generally causing sub-clinical hepatitis with occasional fatalities. EqHV is reported in equids worldwide, but for Italy data are limited. To address this, a survey study was set up to estimate prevalence at a national level and among different production categories (equestrian; competition; work and meat; reproduction) and national macro-regions (North, Central, South, and Islands). Data obtained testing 1801 horse serum samples by Real-Time RT PCR were compared within the categories and regions. The NS3 fragment of the PCR-positive samples was sequenced by Sanger protocol for phylogenetic and mutational analysis. The tertiary structure of the NS3 protein was also assessed. The estimated national prevalence was 4.27% [1.97–6.59, 95% CI] and no statistical differences were detected among production categories and macro-regions. The phylogenesis confirmed the distribution in Italy of the three known EqHV subtypes, also suggesting a possible fourth sub-type that, however, requires further confirmation. Mutational profiles that could also affect the NS3 binding affinity to the viral RNA were detected. The present paper demonstrates that EqHV should be included in diagnostic protocols when investigating causes of hepatitis, and in quality control protocols for blood derived products due to its parental transmission. [ABSTRACT FROM AUTHOR]

Climate change has led to the spread of plant pathogens in novel environments, causing dramatic crop losses and economic damage. Botryosphaeriaceae represents a massive fungal family, containing a huge number of plant pathogens, which are able to infect several hosts. Among them, Macrophomina phaseolina is a necrotrophic fungus, responsible for several plant diseases, including the soft stem rot of common bean, crown rot on strawberry and charcoal rot of several legumes. Here, Macrophomina, causing crown charcoal rot in chickpeas, was isolated from symptomatic plants in Cicerale (SA), Campania, South Italy. Morphological and molecular characterization was carried out and pathogenicity tests were performed. Phylogenetic analyses were performed comparing Macrophomina strains coming from different geographic areas and hosts. The experiments confirmed the pathogenicity of the isolate CREA OF 189.2 on chickpea, while host range highlighted the polyphagous nature of this strain; thus, symptoms were reported on lentils, common bean and cantaloupe. The multidisciplinary approach allows us to increase the knowledge about this emerging pathogen. To the best of our knowledge, this is the first report on Macrophomina phaseolina from chickpeas in Italy. [ABSTRACT FROM AUTHOR]

Lagoviruses are viruses of the Caliciviridae family affecting lagomorphs. Both pathogenic and non-pathogenic lagoviruses affect the European rabbit (Oryctolagus cuniculus), and they are phylogenetically distinguished. Rabbit Hemorrhagic Disease Virus (RHDV/GI.1) and Rabbit Hemorrhagic Disease Virus-2 (RHDV-2/GI.2) belong to the first group, while in the second group, several genotypes of Rabbit Calicivirus (RCV/GI.3-GI.4) are present. The first RCV strain was described in Italy in 1996, and since then, several RCV strains have been characterised in Europe and Australia. RCVs, different from the pathogenic hepatotropic RHDVs, have an enteric tropism and could be identified from the duodenum/intestine and faeces. This study aimed firstly to indirectly show through a seroepidemiological survey from 1998 to 2008 the circulation of RCVs strains in rabbit farms and then to genetically characterise RCV strains diagnosed in Italy in faecal and intestinal samples of wild and farmed rabbits collected in various regions in the following years (2000-2022). Of 262 analysed samples, 69 resulted in RT-PCR positive for lagovirus but negative for RHDV. Eleven RCV strains were characterised by complete vp60 sequencing. Phylogenetic analysis showed that the Italian RCV strains are grouped in European (RCV_E1/GI.3) and Australian (RCV_E2/GI.4) RCV clusters, with an estimated country prevalence of 26%. Based on the proposed genotype classification, considering the nucleotide differences of vp60 higher than 15%, we can hypothesise that two other genotypes, GI.5 and GI.6, might exist within the cluster of non-pathogenic viruses., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethics declarations: Ethical review and approval were waived for this study that did not involve killing animals. The samples did not originate from experimental trials. Still, they took advantage of diagnostic activity conducted on found dead animals to ascertain the cause of death or as a control of the health status of regularly slaughtered rabbits for human meat consumption. Therefore, since the sampling was not specifically programmed as an experimental study but originating from diagnostic activity, we believed that it does not fall under the provisions of the National Law (e.g. DLSG 4/3 2014, n. 26. Application at the national level of the EU Directive 2010/63/UE) and no ethical approval or permit for animal experimentation was required., (© 2024. The Author(s).)

Shiga toxin-producing Escherichia coli (STEC) O80:H2 has emerged in Europe as a cause of hemolytic uremic syndrome associated with bacteremia. STEC O80:H2 harbors the mosaic plasmid pR444_A, which combines several virulence genes, including hlyF and antimicrobial resistance genes. pR444_A is found in some extraintestinal pathogenic E. coli (ExPEC) strains. We identified and characterized 53 STEC strains with ExPEC-associated virulence genes isolated in Italy and the Netherlands during 2000-2019. The isolates belong to 2 major populations: 1 belongs to sequence type 301 and harbors diverse stx2 subtypes, the intimin variant eae-ξ, and pO157-like and pR444_A plasmids; 1 consists of strains belonging to various sequence types, some of which lack the pO157 plasmid, the locus of enterocyte effacement, and the antimicrobial resistance-encoding region. Our results showed that STEC strains harboring ExPEC-associated virulence genes can include multiple serotypes and that the pR444_A plasmid can be acquired and mobilized by STEC strains. [ABSTRACT FROM AUTHOR]

Background The pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains unclear. We report the detection of viral RNA from different anatomical districts and the antibody profile in the first 2 COVID-19 cases diagnosed in Italy. Methods We tested for SARS-CoV-2 RNA clinical samples, either respiratory and nonrespiratory (ie, saliva, serum, urine, vomit, rectal, ocular, cutaneous, and cervico-vaginal swabs), longitudinally collected from both patients throughout the hospitalization. Serological analysis was carried out on serial serum samples to evaluate IgM, IgA, IgG, and neutralizing antibody levels. Results SARS-CoV-2 RNA was detected since the early phase of illness, lasting over 2 weeks in both upper and lower respiratory tract samples. Virus isolate was obtained from acute respiratory samples, while no infectious virus was rescued from late respiratory samples with low viral RNA load, collected when serum antibodies had been developed. Several other specimens came back positive, including saliva, vomit, rectal, cutaneous, cervico-vaginal, and ocular swabs. IgM, IgA, and IgG were detected within the first week of diagnosis, with IgG appearing earlier and at higher titers. Neutralizing antibodies developed during the second week, reaching high titers 32 days after diagnosis. Conclusions Our longitudinal analysis showed that SARS-CoV-2 RNA can be detected in different body samples, which may be associated with broad tropism and different spectra of clinical manifestations and modes of transmission. Profiling antibody response and neutralizing activity can assist in laboratory diagnosis and surveillance actions. [ABSTRACT FROM AUTHOR]

Porcine circovirus type 2 (PCV-2) is among the most burdensome viruses of the swine industry globally. Several genotypes have been periodically emerging, but just three of them (PCV-2a, PCV-2b, and PCV-2d) seem to circulate worldwide and be associated with the disease. Conversely, the spatial-temporal distribution of minor genotypes appears limited and their clinical relevance is still unclear. Recently PCV-2e was incidentally detected for the first time in Europe in a breeding farm in Northeastern Italy, while no connection could be established with countries where this genotype had been previously detected. To investigate circulating genotypes in the neglected rural context and provide a comparison with the most explored industrial context, a molecular survey was performed on samples collected in rural (n = 72) and industrial farms (n = 110) located in the same geographic area. Phylogenetic analysis surprisingly evidenced PCV-2e circulation only in pigs reared in backyard farms (n = 5), while major genotypes (PCV-2a, -2b, -2d) circulate in both rearing contexts. However, the close genetic similarity between the herein detected PCV-2e strains and the previously reported one testify that, although unusual, such rural-to-industrial strains exchange affected also PCV-2e. The greater genetic and phenotypic diversity of PCV-2e genotype compared to other ones might threaten the protection granted by current vaccines. The present study suggests the rural context as an ecological niche for the circulation of PCV-2e, and even of other minor genotypes. PCV-2e detection in pigs with outdoor access further stresses the epidemiological role of backyard farms as interfaces for pathogen introduction, potentially ascribable to the different rearing approaches, lower managerial and biosecurity capabilities, and easier contacts with wildlife., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Since 1996 a new Infectious Bronchitis virus (IBV) genotype, referred to as Q1, circulated in China and was reported for the first time in Italy in 2011, associated with an increase of mortality, kidney lesions and proventriculitis. During northern Italian outbreak of respiratory disease in a broiler flock in 2013, an IBV strain was detected by RT-PCR and characterized as Q1-like based on partial S1 sequence. The virus was isolated and named γCoV/Ck/Italy/I2022/13. All coding regions of the isolate were sequenced and compared with 130 complete genome sequences of IBV and TCoV, downloaded from ViPR. This showed the highest identity with a Chinese strain CK/CH/LDL/97I ( p -distance = 0.044). To identify potential recombination events a complete genome SimPlot analysis was carried out which revealed the presence of possible multiple recombination events, but the minor parent strains remained unknown. A phylogenetic analysis of the complete S1 gene was performed using all complete S1 sequences available on ViPR and showed the isolate clustered with an Q1-like strain isolated in Italy in 2011 ( p -distance = 0.004) and a group of Chinese Q1-like strains isolated from the mid 90's ( p -distance equal or higher than 0.001). It could be hypothesized that the isolate descended from the Italian 2011 Q1-like strain or was the result of a separate introduction from China through commercial trade or migratory birds; but the data currently available does not distinguish between these possibilities. [ABSTRACT FROM AUTHOR]

Abstract: Background: Some diagnostic, epidemiological and clinical features of the recently discovered human metapneumovirus remain to be investigated. Objectives: To study the best approach for the diagnosis of human metapneumovirus infections by both conventional and molecular methods, along with the human metapneumovirus circulation rate in northern Italy and the severity of human metapneumovirus respiratory infections in a pediatric patient population. Study design: Nasopharyngeal aspirates (NPA) were taken from 306 pediatric patients during the winter–spring season 2003–2004, and examined for conventional respiratory viruses by direct fluorescent staining and cell culture, while human coronavirus and human metapneumovirus were sought by RT-PCR. Results: RT-PCR detected human metapneumovirus in 40/306 (13.1%) children positive for respiratory viruses, with an incidence intermediate between that of respiratory syncytial virus (58 patients, 18.9%) and that of influenzavirus infections (29 patients, 9.5%). Phylogenetic analysis showed cocirculation of both human metapneumovirus types (A and B) as well as their relevant subtypes (A1–A2 and B1–B2). Clinically, human metapneumovirus was found to be second to human respiratory syncytial virus alone, as a cause of respiratory tract infections, while duration of virus excretion appeared to correlate with severity of infection, and virus load in NPA with the stage of respiratory infection. Conclusion: (i) Human metapneumovirus is a major viral pathogen in the Italian pediatric patient population; (ii) the severity of lower respiratory tract infections approaches that of human respiratory syncytial virus; (iii) there are preliminary indications that the duration of virus excretion may reach 2–3 weeks and that the level of viral load in NPA correlates with the clinical stage of human metapneumovirus infection. [Copyright &y& Elsevier]

Simple Summary: The genus Circovirus groups some of the smallest viruses capable of autonomous replication, including some notable swine and avian pathogens. Among domestic and wild birds, circoviruses are often associated with immunosuppression and integumental disorders, but, despite their relevance, nothing is known about their circulation in birds of prey. By conducting molecular analyses on samples from birds of prey recovered by a wildlife rescue centre in Italy, we identified a new viral species in the spleen of a tawny owl (Strix aluco). However, there is contrasting evidence regarding its definitive host. On one hand, the virus was discovered to be phylogenetically closer to mammalian rather than avian circoviruses, which allows speculations on its host being a micromammal preyed by the tawny owl, rather than the bird itself. On the other hand, its detection in the spleen, a lymphoid organ in which other avian circoviruses are often detected, supports the tawny owl being its actual host, perhaps following a spillover event associated with predation. Adding to the growing number of circoviruses found in recent years in a diverse range of hosts, this discovery represents another step forward in the characterization of this genus of remarkable veterinary importance. Thanks to recent developments in molecular methods, many new species have been discovered within the genus Circovirus, which comprises viruses of veterinary relevance found in a broad range of hosts. In particular, several circoviruses are known to infect birds, often causing immunosuppression and feathering disorders. Nonetheless, nothing is known about their circulation in birds of prey. In this study, samples from 61 birds of prey representing ten different species, recovered by a wildlife rescue centre in Southern Italy, were taken at necropsy and analysed by PCR with pan-Circovirus primers. Only one sample, collected from a tawny owl (Strix aluco), tested positive. Its genome, sequenced by primer walking, displays the typical features of circoviruses. Based on demarcation criteria, the detected strain qualifies as a novel species, which was named "tawny owl-associated circovirus" (ToCV). Phylogenetically, ToCV clustered with mammalian rather than avian circoviruses, and its closeness to a rodent circovirus suggests that its host may have been a micromammal eaten by the tawny owl. On the other hand, its detection in the spleen fits with the tropism of other avian circoviruses. Little can be therefore said on its biology and pathogenicity, and further efforts are needed to better characterize its epidemiology. [ABSTRACT FROM AUTHOR]

• First detection and genetic characterisation of the PCV-2e genotype in Europe. • PCV-2e was detected in the absence of PCV disease-related clinical signs in Italian sows. • Follow-up breeder herd study demonstrated persistent PCV-2e subclinical circulation. • More intensive monitoring activities of asymptomatic animals is needed. • Efficacy of current vaccines and diagnostic tools requires further evaluation. 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. [ABSTRACT FROM AUTHOR]

Genotype screening was implemented in Italy and showed a significant prevalence of new SARS-CoV-2 mutants carrying Q675H mutation, near the furin cleavage site of spike protein. Currently, this mutation, which is expressed on different SARS-CoV-2 lineages circulating worldwide, has not been thoughtfully investigated. Therefore, we performed phylogenetic and biocomputational analysis to better understand SARS-CoV-2 Q675H mutants' evolutionary relationships with other circulating lineages and Q675H function in its molecular context. Our studies reveal that Q675H spike mutation is the result of parallel evolution because it arose independently in separate evolutionary clades. In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region. This results in an optimized directionality of arginine residues involved in interaction of spike with the furin binding pocket, thus improving proteolytic exposure of the viral protein. Furin was predicted to have a greater affinity for Q675H than Q675 substrate conformations. As a consequence, Q675H mutation could confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. Interestingly, here we have shown that Q675H spike mutation is documented in all the VOCs. This finding highlights that VOCs are still evolving to enhance viral fitness and to adapt to the human host. At the same time, it may suggest Q675H spike mutation involvement in SARS-CoV-2 evolution. [ABSTRACT FROM AUTHOR]

Aelurostrongylus abstrusus (Nematoda, Strongylida) lives in the terminal respiratory bronchioles and alveolar ducts of cats. The infection may present with respiratory signs of varying severity and can be life threatening. Despite the importance of A. abstrusus in feline medicine and recent reports of clinical cases of aelurostrongylosis in Italy, epidemiological data are sparse and molecular information available on the parasite are lacking. The present work reports recent insights into the epidemiology of feline lungworm infection in Italy and contributes to the molecular knowledge of A. abstrusus. Individual stool samples were collected from 100 animals and examined with flotation and Baermann methods. The risk factors were analyzed by binary logistic multiple-regression models. All positive fecal samples ( n= 16) were subjected to the PCR-coupled sequencing of the rDNA internal trancribed spacer 2 (ITS2). The detected infection rate differs significantly from data reported in the literature, and stray and free-ranging cats and the presence of respiratory symptoms were risk factors for the infection. The molecular characterization showed that the ITS2 sequence is a promising genetic target for a holistic approach to the study of cat lungworm infection. Epidemiological and molecular insights and avenues are discussed. [ABSTRACT FROM AUTHOR]

Simple Summary: Tick-borne infectious diseases represent a rising threat both for human and animal health, since they are emerging worldwide. Among the bacterial infections, Anaplasma phagocytophilum has been largely neglected in Europe. Despite its diffusion in ticks and animals, the ecoepidemiology of its genetic variants is not well understood. The latest studies identify four ecotypes of Anaplasma phagocytophilum in Europe, and only ecotype I has shown zoonotic potential. The aim of the present study was to investigate the genetic variants of Anaplasma phagocytophilum in wild ungulates, the leading reservoir species, and in feeding ticks, the main vector of infection. The analyzed samples were collected in northeastern Italy, the same area where the first Italian human cases of anaplasmosis in the country were reported. Using biomolecular tools and phylogenetic analysis, ecotypes I and II were detected in both ticks (Ixodes ricinus species) and wild ungulates. Specifically, ecotype II was mainly detected in roe deer and related ticks; and ecotype I, the potentially zoonotic variant, was detected in Ixodes ricinus ticks and also in roe deer, red deer, chamois, mouflon, and wild boar. These findings reveal not only the wide diffusion of Anaplasma phagocytophilum, but also the presence of zoonotic variants. Anaplasma phagocytophilum (A. phagocytophilum) is a tick-borne pathogen causing disease in both humans and animals. Human granulocytic anaplasmosis (HGA) is an emerging disease, but despite the remarkable prevalence in European ticks and wild animals, human infection appears underdiagnosed. Several genetic variants are circulating in Europe, including the zoonotic ecotype I. This study investigated A. phagocytophilum occurrence in wild ungulates and their ectoparasites in an area where HGA has been reported. Blood samples from wild ungulates and ectoparasites were screened by biomolecular methods targeting the mps2 gene. The groEL gene was amplified and sequenced to perform genetic characterization and phylogenetic analysis. A total of 188 blood samples were collected from different wild ungulates species showing an overall prevalence of 63.8% (88.7% in wild ruminants and 3.6% in wild boars). The prevalence of A. phagocytophilum DNA in ticks (manly Ixodes ricinus), and keds collected from wild ruminants was high, reflecting the high infection rates obtained in their hosts. Among ticks collected from wild boars (Hyalomma marginatum and Dermacentor marginatus) no DNA was detected. Phylogenetic analysis demonstrated the presence of ecotype I and II. To date, this is the first Italian report of ecotype I in alpine chamois, mouflon, and wild boar species. These findings suggest their role in HGA epidemiology, and the high prevalence detected in this study highlights that this human tick-borne disease deserves further attention. [ABSTRACT FROM AUTHOR]