116 results on '"Ilaria Di Bartolo"'
Search Results
2. Investigating the Hepatitis E Virus (HEV) Diversity in Rat Reservoirs from Northern Italy
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Luca De Sabato, Marina Monini, Roberta Galuppi, Filippo Maria Dini, Giovanni Ianiro, Gabriele Vaccari, Fabio Ostanello, and Ilaria Di Bartolo
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hepatitis E virus ,reservoir ,rat ,zoonoses ,HEV-C1 ,Italy ,Medicine - Abstract
Hepatitis E virus belonging to the Rocahepevirus ratti species, genotype HEV-C1, has been extensively reported in rats in Europe, Asia and North America. Recently, human cases of hepatitis associated with HEV-C1 infection have been reported, but the zoonotic nature of rat-HEV remains controversial. The transmission route of rat-HEV is unidentified and requires further investigation. The HEV strains of the Paslahepevirus balayani species, belonging to the same Hepeviridae family, and including the zoonotic genotype HEV-3 usually found in pigs, have also sporadically been identified in rats. We sampled 115 rats (liver, lung, feces) between 2020 and 2023 in Northeast Italy and the HEV detection was carried out by using Reverse Transcription PCR. HEV RNA was detected in 3/115 (2.6%) rats who tested positive for HEV-C1 strains in paired lung, intestinal contents and liver samples. Overall, none tested positive for the Paslahepevirus balayani strains. In conclusion, our results confirm the presence of HEV-rat in Italy with a prevalence similar to previous studies but show that there is a wide heterogeneity of strains in circulation. The detection of HEV-C1 genotype of Rocahepevirus ratti species in some human cases of acute hepatitis suggests that HEV-C1 may be an underestimated source of human infections. This finding, with the geographically widespread detection of HEV-C1 in rats, raises questions about the role of rats as hosts for both HEV-C1 and HEV-3 and the possibility of zoonotic transmission.
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- 2024
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3. Exploring the Potential of Muridae as Sentinels for Human and Zoonotic Viruses
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Ilaria Di Bartolo, Luca De Sabato, Giovanni Ianiro, Gabriele Vaccari, Filippo Maria Dini, Fabio Ostanello, and Marina Monini
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Muridae ,rats ,mice ,viral zoonoses ,rodents ,reservoir ,Microbiology ,QR1-502 - Abstract
In recent years, the transmission of viruses from wildlife to humans has raised significant public health concerns, exemplified by the COVID-19 pandemic caused by the betacoronavirus SARS-CoV-2. Human activities play a substantial role in increasing the risk of zoonotic virus transmission from wildlife to humans. Rats and mice are prevalent in urban environments and may act as reservoirs for various pathogens. This study aimed to evaluate the presence of zoonotic viruses in wild rats and mice in both urban and rural areas, focusing on well-known zoonotic viruses such as betacoronavirus, hantavirus, arenavirus, kobuvirus, and monkeypox virus, along with other viruses occasionally detected in rats and mice, including rotavirus, norovirus, and astrovirus, which are known to infect humans at a high rate. A total of 128 animals were captured, including 70 brown rats (Rattus norvegicus), 45 black rats (Rattus rattus), and 13 house mice (Mus musculus), and feces, lung, and liver were collected. Among brown rats, one fecal sample tested positive for astrovirus RNA. Nucleotide sequencing revealed high sequence similarity to both human and rat astrovirus, suggesting co-presence of these viruses in the feces. Murine kobuvirus (MuKV) was detected in fecal samples from both black (n = 7) and brown (n = 6) rats, primarily from urban areas, as confirmed by sequence analysis. These findings highlight the importance of surveillance and research to understand and mitigate the risks associated with the potential transmission of pathogens by rodents.
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- 2024
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4. Identification of Aichivirus in a Pet Rat (Rattus norvegicus) in Italy
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Flora Alfano, Maria Gabriella Lucibelli, Francesco Serra, Martina Levante, Simona Rea, Amalia Gallo, Federica Petrucci, Alessia Pucciarelli, Gerardo Picazio, Marina Monini, Ilaria Di Bartolo, Dario d’Ovidio, Mario Santoro, Esterina De Carlo, Giovanna Fusco, and Maria Grazia Amoroso
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aichivirus ,Rattus norvegicus ,exotic pets ,kobuvirus ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
We investigated the occurrence of eight potential zoonotic viruses in 91 exotic companion mammals from pet shops in southern Italy via real-time PCR and end-point PCR. The animals were screened for aichivirus, sapovirus, astrovirus, hepatitis A, noroviruses (GI and GII), rotavirus, circovirus, and SARS-CoV-2. Among the nine species of exotic pets studied, only one rat tested positive for aichivirus. The high sequence similarity to a murine kobuvirus-1 strain previously identified in China suggests that the virus may have been introduced into Italy through the importation of animals from Asia. Since exotic companion mammals live in close contact with humans, continuous sanitary monitoring is crucial to prevent the spread of new pathogens among domestic animals and humans. Further investigations on detecting and typing zoonotic viruses are needed to identify emerging and re-emerging viruses to safeguard public health.
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- 2024
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5. Biosecurity measures to control hepatitis E virus on European pig farms
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Tamino Dubbert, Marina Meester, Richard Piers Smith, Tijs J. Tobias, Ilaria Di Bartolo, Reimar Johne, Enrico Pavoni, Gergana Krumova-Valcheva, Elena Lucia Sassu, Christopher Prigge, Giuseppe Aprea, Hannah May, Nadine Althof, Giovanni Ianiro, Jacek Żmudzki, Albena Dimitrova, Giovanni Loris Alborali, Daniela D'Angelantonio, Silvia Scattolini, Noemi Battistelli, and Elke Burow
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hepatitis-E-virus ,HEV ,biosecurity measures ,pig production ,BIOPIGEE ,One Health ,Veterinary medicine ,SF600-1100 - Abstract
Hepatitis E virus (HEV) genotype 3 is a prevalent zoonotic pathogen in European pig farms, posing a significant public health risk primarily through the foodborne route. The study aimed to identify effective biosecurity measures for controlling HEV transmission on pig farms, addressing a critical gap in current knowledge. Utilizing a cross-sectional design, fecal samples from gilts, dry sows, and fatteners were collected on 231 pig farms of all farm types across nine European countries. Real-time RT-PCR was employed to test these samples for HEV. Simultaneously, a comprehensive biosecurity questionnaire captured data on various potential measures to control HEV. The dependent variable was HEV risk, categorized as lower or higher based on the percentage of positive pooled fecal samples on each farm (25% cut-off). The data were analyzed using generalized linear models (one for finisher samples and one for all samples) with a logit link function with country and farm type as a priori fixed factors. The results of the final multivariable models identified key biosecurity measures associated with lower HEV risk, which were the use of a hygienogram in the breeding (OR: 0.06, p = 0.001) and/or fattening area after cleaning (OR: 0.21, p = 0.019), the presence of a quarantine area (OR: 0.29, p = 0.025), testing and/or treating purchased feed against Salmonella (OR: 0.35, p = 0.021), the presence of other livestock species on the farm, and having five or fewer persons in charge of the pigs. Contrary to expectations, some biosecurity measures were associated with higher HEV risk, e.g., downtime of 3 days or longer after cleaning in the fattening area (OR: 3.49, p = 0.005) or mandatory handwashing for farm personnel when changing barn sections (OR: 3.4, p = 0.026). This novel study unveils critical insights into biosecurity measures effective in controlling HEV on European pig farms. The identification of both protective and risk-associated measures contributes to improving strategies for managing HEV and underscores the complexity of biosecurity in pig farming.
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- 2024
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6. Selective Pressure and Evolution of SARS-CoV-2 Lineages BF.7 and BQ.1.1 Circulating in Italy from July to December 2022
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Alessandra Lo Presti, Luigina Ambrosio, Angela Di Martino, Arnold Knijn, Luca De Sabato, Gabriele Vaccari, Ilaria Di Bartolo, Stefano Morabito, Anna Teresa Palamara, Paola Stefanelli, and on behalf of the Italian Genomic Laboratory Network
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genetic diversity ,mutation ,phylogenetic analysis ,SARS-CoV-2 ,selective pressure ,Biology (General) ,QH301-705.5 - Abstract
In this work, we studied the selective pressure and evolutionary analysis on the SARS-CoV-2 BF.7 and BQ.1.1 lineages circulating in Italy from July to December 2022. Two different datasets were constructed: the first comprised 694 SARS-CoV-2 BF.7 lineage sequences and the second comprised 734 BQ.1.1 sequences, available in the Italian COVID-19 Genomic (I-Co-Gen) platform and GISAID (last access date 15 December 2022). Alignments were performed with MAFFT v.7 under the Galaxy platform. The HYPHY software was used to study the selective pressure. Four positively selected sites (two in nsp3 and two in the spike) were identified in the BF.7 dataset, and two (one in ORF8 and one in the spike gene) were identified in the BQ.1.1 dataset. Mutation analysis revealed that R408S and N440K are very common in the spike of the BF.7 genomes, as well as L452R among BQ.1.1. N1329D and Q180H in nsp3 were found, respectively, at low and rare frequencies in BF.7, while I121L and I121T were found to be rare in ORF8 for BQ.1.1. The positively selected sites may have been driven by the selection for increased viral fitness, under circumstances of defined selective pressure, as well by host genetic factors.
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- 2024
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7. A Review of Slaughter Practices and Their Effectiveness to Control Microbial – esp. Salmonella spp. – Contamination of Pig Carcasses
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Arvo Viltrop, Tarmo Niine, Tijs Tobias, Elena Lucia Sassu, Ilaria Di Bartolo, Enrico Pavoni, Giovanni Loris Alborali, Elke Burow, and Richard Piers Smith
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Abattoir ,Biosecurity ,Slaughter hygiene ,Swine ,Pork ,Hepatitis E virus ,Food processing and manufacture ,TP368-456 ,Nutrition. Foods and food supply ,TX341-641 - Abstract
The BIOPIGEE project (part of the One Health European Joint Programme under Horizon 2020) aimed to identify relevant measures to effectively control Salmonella, and another zoonotic pathogen, hepatitis E virus (HEV) within the pig meat food chain. The aim of this study was to identify biosecurity measures or management practices that are relevant for limiting Salmonella and/or HEV occurrence and spread within pig slaughterhouses. This was with the final goal of compiling a list of biosecurity measures for different processes and operations along the slaughter line with evidence of their effectiveness. To achieve this, a literature review was conducted on studies estimating the effectiveness of measures applied in slaughterhouses to reduce the microbial contamination of pig carcasses. Results of this literature search are discussed and presented in summary tables that could be used as a source of information for the pig slaughter industry to further develop their guidelines on hygienic slaughter.
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- 2023
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8. First serological and molecular investigation of hepatitis E virus infection in dromedary camels in Algeria
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Amir Agabou, Mohamed Hocine Benaissa, Ilyes Bouasla, Luca De Sabato, Sana Hireche, Giovanni Ianiro, Marina Monini, and Ilaria Di Bartolo
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hepatitis E virus ,ELISA ,seroprevalence ,risk factors ,dromedary camels ,Algeria ,Veterinary medicine ,SF600-1100 - Abstract
Hepatitis E is an acute self-limited or fulminant infection in humans, caused by the hepatitis E virus (HEV). This member of the Hepeviridae family has been identified in a wide range of domestic and wild animals all over the world, with a possible transmission to humans through fecal oral route, direct contact and ingestion of contaminated meat products, making it one of the global zoonotic and public health major concerns. Since there is no monitoring program and a lack of data on HEV in animals in Algeria, the current preliminary survey has been undertaken to elucidate the exposure to the virus in camels at abattoirs of six southern provinces of Algeria. Two-hundred and eight sera/plasma were collected and analyzed (by double antigen sandwich ELISA) for the presence of total anti-HEV antibodies, among which 35.1% were positive, but no HEV RNA could be isolated from them (by two pan-HEV nested RT-PCR and broad range real-time reverse transcription RT-PCR). The univariate analysis showed significant associations (p
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- 2023
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9. Erinaceus coronavirus persistence in hedgehogs (Erinaceus europaeus) in a non-invasive, in vivo, experimental setting
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Luca De Sabato, Giovanni Ianiro, Francesca Manzia, Marina Monini, Barbara Chiappini, Ilaria Di Bartolo, and Gabriele Vaccari
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Merbecovirus ,Erinaceus europaeus ,Erinaceus coronavirus (EriCoV) ,Coronavirus ,European hedgehogs ,Veterinary medicine ,SF600-1100 - Abstract
In the last 20 years, new zoonotic CoV strains have emerged (SARS-CoV, MERS-CoV, and SARS-CoV-2), and new species have also been reported in animals. In Europe, the Erinaceus coronavirus (EriCoV) was recently described in Erinaceus europaeus. However, information on the prevalence and duration of viral shedding is unknown. In this study, feces samples were collected from 102 European hedgehogs hosted in the Center for the Recovery of Wild Fauna in Rome and analyzed for the presence of EriCoV RNA by Reverse Transcription-PCR. In total, 45 animals (44.1%) resulted positive for EriCoV at the first sampling and 63 (61.7%) animals were positive at the follow-up, which was performed from the 3rd to the 86th day. The duration of fecal virus shedding showed a mean duration of 22.8 days and lasted up to 62 days. Eighteen hedgehogs showed intermittent viral shedding. Phylogenetic analysis showed a correlation with EriCoV strains reported in Germany, the United Kingdom, and northern Italy. None of the EriCoV sequences showed the CD200 ortholog insertion, previously observed in strains isolated in animals from northern Italy. Interestingly, all but one animal revealed the presence in their feces of the same EriCoV sequences, analyzing the short genomic region at 3' spike gene and 5' ORF3a 500bp fragment (100% nt.id.) in both first and follow-up samples. This result suggests that animals were infected with the same strain during their stay at the center. Our results confirm that EriCoV can persist in hedgehogs for a long period, underlining that hedgehogs are an important commensal reservoir for Merbecovirus. A long duration of viral shedding increases the likelihood that the virus will spread in the environment.
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- 2023
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10. Cross-sectional study of hepatitis E virus (HEV) circulation in Italian pig farms
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Giovanni Ianiro, Enrico Pavoni, Giuseppe Aprea, Romina Romantini, Giovanni Loris Alborali, Daniela D'Angelantonio, Giuliano Garofolo, Silvia Scattolini, Luca De Sabato, Chiara Francesca Magistrali, Elke Burow, Fabio Ostanello, Richard Piers Smith, and Ilaria Di Bartolo
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hepatitis E virus ,HEV ,zoonoses ,pig ,feces ,farm ,Veterinary medicine ,SF600-1100 - Abstract
Foodborne transmission is considered the main way of spreading zoonotic hepatitis E virus (HEV) infection in Europe. In recent years, the human cases of hepatitis E in subjects without history of travel in endemic areas have raised, suggesting that domestic HEV transmission is increasing. Pork products with or without liver, are often indicated as the source of many human foodborne HEV cases as well as small outbreaks. Pigs are recognized as the main reservoir of the zoonotic HEV-3 genotype, the most frequently detected in human cases in the EU. In the absence of a harmonized surveillance of HEV circulation, data on prevalence are heterogeneous but confirm a widespread circulation of HEV-3 in pig herds across EU. HEV-3 can pass through the food chain from farm to fork when infected animals are slaughtered. In Italy, several studies reported the circulation of HEV-3 in pig farms, but results are heterogeneous due to different methodologies applied. In the present study, we performed a survey over 51 pig herds belonging to three main types of farms: breeding, fattening and farrow-to-finish. HEV-RNA was analyzed by broad range Real-time RT-PCR on 20 samples for each farm, obtained by pooling together feces from 10 individuals. Overall, HEV RNA was confirmed on 150 fecal pooled samples out of 1,032 (14.5%). At least one positive pooled sample was detected from 18 farms out of 51 tested (35.3%). By lowering the number of infected pigs at primary production, the risk of HEV-3 entering into the food chain can be reduced. Hence, information on HEV circulation in herds is highly relevant for choosing preventive measures and deserves development of a monitoring program and further investigations.
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- 2023
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11. Tracking the Selective Pressure Profile and Gene Flow of SARS-CoV-2 Delta Variant in Italy from April to October 2021 and Frequencies of Key Mutations from Three Representative Italian Regions
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Alessandra Lo Presti, Angela Di Martino, Luigina Ambrosio, Luca De Sabato, Arnold Knijn, Gabriele Vaccari, Ilaria Di Bartolo, Stefano Morabito, Calogero Terregino, Alice Fusaro, Isabella Monne, Edoardo Giussani, Fabio Tramuto, Carmelo Massimo Maida, Walter Mazzucco, Claudio Costantino, Martina Rueca, Emanuela Giombini, Cesare Ernesto Maria Gruber, Maria Rosaria Capobianchi, Anna Teresa Palamara, Paola Stefanelli, and on behalf of the Italian Genomic Laboratory Network
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gene flows ,mutations ,SARS-CoV-2 Delta variant ,selective pressure ,Biology (General) ,QH301-705.5 - Abstract
The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions. The selective pressure and the frequency of amino acid substitutions and the prediction of their possible impact on the stability of the proteins were investigated. Delta variant dataset, in this study, identified 68 sites under positive selection: 16 in the spike (23.5%), 11 in nsp2 (16.2%) and 10 in nsp12 (14.7%) genes. Three of the positive sites in the spike were located in the receptor-binding domain (RBD). In Delta genomes from the three regions, 6 changes were identified as very common (>83.7%), 4 as common (>64.0%), 21 at low frequency (2.1%–25.0%) and 29 rare (≤2.0%). The detection of positive selection on key mutations may represent a model to identify recurrent signature mutations of the virus.
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- 2023
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12. Hepatitis E Virus (HEV) in Heavy Pigs in Slaughterhouses of Northern Italy: Investigation of Seroprevalence, Viraemia, and Faecal Shedding
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Marina Monini, Ilaria Di Bartolo, Luca De Sabato, Giovanni Ianiro, Francesca Agostinelli, and Fabio Ostanello
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HEV ,zoonoses ,pigs ,slaughterhouse ,viraemia ,IgM ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
Hepatitis E virus (HEV) is considered an emerging threat in Europe, owing to the increased number of human cases and the widespread presence of the virus in pigs at farms. Most cases in industrialized countries are caused by the zoonotic HEV-3 genotype. The main transmission route of HEV-3 in Europe is foodborne, through consumption of raw or undercooked liver pork and wild boar meat. Pigs become susceptible to HEV infection after the loss of maternal immunity, and the majority of adult pigs test positive for IgG anti-HEV antibodies. Nonetheless, HEV-infected pigs in terms of liver, faeces, and rarely blood are identified at slaughterhouses. The present study aimed to investigate the prevalence of HEV-positive batches of Italian heavy pigs at slaughterhouses, assessing the presence of animals still shedding HEV upon their arrival at the slaughterhouse by sampling faeces collected from the floor of the trucks used for their transport. The occurrence of viraemic animals and the seroprevalence of anti-HEV antibodies were also assessed. The results obtained indicated the presence of anti-HEV IgM (1.9%), and a high seroprevalence of anti-HEV total antibodies (IgG, IgM, IgA; 89.2%, n = 260). HEV RNA was not detected in either plasma or faecal samples. Nevertheless, seropositive animals were identified in all eight batches investigated, confirming the widespread exposure of pigs to HEV at both individual and farm levels. Future studies are needed to assess the factors associated with the risk of HEV presence on farms, with the aim to prevent virus introduction and spread within farms, thereby eliminating the risk at slaughterhouse.
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- 2023
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13. Possible Human-to-Dog Transmission of SARS-CoV-2, Italy, 2020
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Nicola Decaro, Gabriele Vaccari, Alessio Lorusso, Eleonora Lorusso, Luca De Sabato, Edward I. Patterson, Ilaria Di Bartolo, Grant L. Hughes, Liana Teodori, Costantina Desario, Barbara Colitti, Dominga Ricci, Domenico Buonavoglia, Sergio Rosati, Vito Martella, Cesare Cammà, Umberto Agrimi, and Gabriella Elia
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dogs ,humans ,SARS-CoV-2 transmission ,next-generation sequencing ,phylogeny ,SARS-CoV-2 ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
We detected severe acute respiratory syndrome coronavirus 2 in an otherwise healthy poodle living with 4 family members who had coronavirus disease. We observed antibodies in serum samples taken from the dog, indicating seroconversion. Full-length genome sequencing showed that the canine and human viruses were identical, suggesting human-to-animal transmission.
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- 2021
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14. Detection of HEV RNA Using One-Step Real-Time RT-PCR in Farrow-to-Finish Pig Farms in Bulgaria
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Gergana Lyubomirova Krumova-Valcheva, Ilaria Di Bartolo, Richard Piers Smith, Eva Gyurova, Gergana Mateva, Mihail Milanov, Albena Dimitrova, Elke Burow, and Hristo Daskalov
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hepatitis E virus ,farrow-to-finish pig farms ,finishers ,dry sows ,gilts ,one-step real-time RT-PCR ,Medicine - Abstract
(1) Background: HEV is a zoonotic, foodborne pathogen. It is spread worldwide and represents a public health risk. The aim of this study was to evaluate the presence of HEV RNA in farrow-to-finish pig farms in different regions of Bulgaria; (2) Methods: Isolation of HEV RNA from pooled samples of feces was performed using a QIAamp® Viral RNA Mini Kit followed by HEV RNA detection using a single-step real-time RT-PCR with primers and probes targeting the ORF 3 HEV genome; (3) Results: HEV RNA was detected in 12 out of 32 tested farms in Bulgaria (37.5%). The overall percentage of HEV-positive pooled fecal samples was 10.8% (68 of 630 samples). HEV was detected mostly in pooled fecal samples from finisher pigs (66/320, 20.6%) and sporadically from dry sows (1/62, 1.6%) and gilts (1/248, 0.4%); (4) Conclusions: Our results confirm that HEV circulates in farrow-to-finish pig farms in Bulgaria. In our study, we found HEV RNA in pooled fecal samples from fattening pigs (4–6-months age), shortly before their transport to the slaughterhouse indicating a potential risk to public health. The possible circulation of HEV throughout pork production requires monitoring and containment measures.
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- 2023
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15. Absence of Hepatitis E Virus (HEV) in Italian Lagomorph Species Sampled between 2019 and 2021
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Luca De Sabato, Giovanni Ianiro, Virginia Filipello, Sara Arnaboldi, Francesco Righi, Fabio Ostanello, Monica Giammarioli, Antonio Lavazza, and Ilaria Di Bartolo
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hepatitis E virus ,rabbit ,hare ,wild rabbit ,zoonosis ,HEV ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
The zoonotic hepatitis E virus genotype 3 (HEV-3) causes most autochthonous human hepatitis E cases in Europe, which are due to the consumption of raw or undercooked food products of animal origin. Pigs and wild boars are considered the main reservoirs of this genotype, while rabbits are the reservoir of a distinct phylogenetic group named HEV-3ra, which is classified within the HEV-3 genotype but in a separate clade. Evidence for the zoonotic potential of HEV-3ra was suggested by its detection in immunocompromised patients in several European countries. HEV-3ra infection was found in farmed and feral rabbit populations worldwide and its circulation was reported in a few European countries, including Italy. Furthermore, Italy is one of the major rabbit meat producers and consumers across Europe, but only a few studies investigated the presence of HEV in this reservoir. The aim of this study was to assess the presence of HEV in 328 Italian hares and 59 farmed rabbits collected in 3 Italian macro-areas (North, North-Central, and South-Central), between 2019 and 2021. For this purpose, liver samples were used to detect HEV RNA using broad-range real-time RT-PCR and nested RT-PCR. Using 28 liver transudates from hares, the ELISA test for anti-HEV IgG detection was also performed. Neither HEV RNA nor anti-HEV antibodies were detected. Further studies will be conducted to assess the HEV presence in Italian lagomorphs to establish the role of this host and the possible risk of transmission for workers with occupational exposure, to pet owners and via food.
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- 2023
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16. In Vitro Replication of Swine Hepatitis E Virus (HEV): Production of Cell-Adapted Strains
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Giovanni Ianiro, Marina Monini, Maria Grazia Ammendolia, Luca De Sabato, Fabio Ostanello, Gabriele Vaccari, and Ilaria Di Bartolo
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HEV ,subtype ,HEV-3 ,A549 ,isolate ,cell culture ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
The hepatitis E caused by the virus HEV of genotypes HEV-3 and HEV-4 is a zoonotic foodborne disease spread worldwide. HEV is currently classified into eight different genotypes (HEV-1–8). Genotypes HEV-3 and HEV-4 are zoonotic and are further divided into subtypes. Most of the information on HEV replication remains unknown due to the lack of an efficient cell cultivation system. Over the last couple of years, several protocols for HEV cultivation have been developed on different cell lines; even if they were troublesome, long, and scarcely reproducible, they offered the opportunity to study the replicative cycle of the virus. In the present study, we aimed to obtain a protocol ready to use viral stock in serum free medium that can be used with reduced time of growth and without any purification steps. The employed method allowed isolation and cell adaptation of four swine HEV-3 strains, belonging to three different subtypes. Phylogenetic analyses conducted on partial genome sequences of in vitro isolated strains did not reveal any insertion in the hypervariable region (HVR) of the genomes. A limited number of mutations was acquired in the genome during the virus growth in the partial sequences of Methyltransferase (Met) and ORF2 coding genes.
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- 2023
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17. The role of staff and contaminated environmental surfaces in spreading of norovirus infection in a long-term health care facility in Italy
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Giuseppe Aprea, Ilaria Di Bartolo, Marina Monini, Daniela D’Angelantonio, Silvia Scattolini, Arianna Boni, Gennaro Truglio, Silvia Di Giacobbe, Annalisa Serio, Salvatore Antoci, Violeta Di Marzio, Giacomo Migliorati, Nicola D'Alterio, and Francesco Pomilio
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long term care facility ,norovirus GII.4 ,outbreak ,surface contamination ,Animal culture ,SF1-1100 ,Veterinary medicine ,SF600-1100 - Abstract
Some residents and people from the staff of a geriatric health care facility in Teramo province, developed acute gastroenteritis from March 8th to March 21st 2017. A prompt epidemiological investigation was conducted to identify the etiological agent, the trace back the potential ways of transmission and control the infection. Information on the outbreak was collected through an epidemiological questionnaire. Faecal samples from all human cases (n = 50) and swabs from environmental surfaces were collected and analysed by RT-PCR for the presence of Norovirus (NoV). Among faecal samples, 34 out of 50 were positive for NoV with no other pathogen detected. In particular, 2 (2/34) were positive to NoV genogroup I (GI), 31 (31/34) to NoV genogroup II (GII), and one sample (1/34) was positive to both NoV GI and GII. Moreover, faecal samples of people from the canteen (n = 8) were also tested resulting negative to NoV detection. Norovirus was also detected in 28 of the 122 swabs from environmental surfaces collected. Among the positive samples, 12 NoV strains were subtyped as NoV GII.4 Sydney_2012 variant. Person-to-person close contact and contaminated environmental surfaces were the probable transmission route among the people of the health care facility. The members of the staff were considered to play an important role in transmission of NoV. A proper disinfection procedure applied during the outbreak could have been critically important to limit the dissemination of the viral infection.
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- 2021
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18. SARS-CoV-2 in a Mink Farm in Italy: Case Description, Molecular and Serological Diagnosis by Comparing Different Tests
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Ana Moreno, Davide Lelli, Tiziana Trogu, Antonio Lavazza, Ilaria Barbieri, MariaBeatrice Boniotti, Giulia Pezzoni, Cristian Salogni, Stefano Giovannini, Giovanni Alborali, Silvia Bellini, Massimo Boldini, Marco Farioli, Luigi Ruocco, Olivia Bessi, Andrea Maroni Ponti, Ilaria Di Bartolo, Luca De Sabato, Gabriele Vaccari, Gabriele Belli, Alberto Margutti, and Maurilio Giorgi
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SARS-CoV-2 diagnosis ,serology ,phylogenetic analysis ,mink farm ,Italy ,Microbiology ,QR1-502 - Abstract
This study described a SARS-CoV-2 infection in minks on an Italian farm. Surveillance was performed based on clinical examination and a collection of 1879 swabs and 74 sera from dead and live animals. The farm was placed under surveillance for 4.5 months, from the end of July 2020, when a man working on the farm tested positive by RT-PCR, till mid-December 2020 when all the animals were sacrificed. Clinical examination revealed no clinical signs or increased mortality rates attributable to SARS-CoV-2, while diagnostic tests detected only four weak PCR-positive samples, but 100% of sera were positive for SARS-CoV-2 anti-S antibodies. The phylogenetic analysis of two SARS-CoV-2 sequences from two minks and the sequence of the worker showed that they belonged to different clades. It could be therefore assumed that two distinct introductions of the virus occurred on the farm, and that the first introduction probably occurred before the start of the surveillance period. From the data collected, and especially from the detection of specific antibodies through the combination of different tests, it can be postulated that syndromic surveillance combined with genome detection by PCR may not be sufficient to achieve a diagnosis in asymptomatic animals. In particular, the serological approach, especially when using tests directed towards the S protein, may be useful for improving the traceability of virus circulation in similar environments.
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- 2022
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19. Dynamic of Hepatitis E Virus (HEV) Shedding in Pigs
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Giovanni Ianiro, Marina Monini, Luca De Sabato, Eleonora Chelli, Natalino Cerini, Fabio Ostanello, and Ilaria Di Bartolo
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HEV ,swine ,pigs ,fatteners ,foodborne ,risk ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
Genotype 3 of hepatitis E virus (HEV-3) is the most common in Europe in both humans and pigs. HEV-3 strains are zoonotic, and foodborne cases associated with consumption of raw and undercooked pork products, mainly liver sausages, have been described. HEV-3 circulates largely in European pig farms, maybe due to its long persistence in the environment. Animals get infected around 3–4 months of age; shortly after, the infection starts to decline up to the age of slaughtering (8–9 months of age in Italy). With the purpose to understand the duration in farmed pigs of the shedding of the virus and its quantity, HEV-RNA detection was performed by Real-time RT-PCR from feces collected individually from two groups of 23 pigs. Sampling was conducted for 4 months shortly before slaughtering age. At 4-months-old, all animals were shedding HEV-3 to high load around 105 genome copies per gram (GC/g). Prevalence was higher in growers than in fatteners, with most of the pigs still positive around 166 days of age. Beyond some difference among individual pigs, the amount of HEV in feces decreased with the age of animals. The longest fattening period should ensure a lower risk of HEV shedder animals at slaughter, reducing the risk of food contamination.
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- 2022
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20. Molecular Characterization of HEV Genotype 3 in Italy at Human/Animal Interface
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Luca De Sabato, Ilaria Di Bartolo, Daniele Lapa, Maria Rosaria Capobianchi, and Anna Rosa Garbuglia
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hepatitis E virus ,hepatitis E ,subtype ,prevalence ,zoonosis ,Italy ,Microbiology ,QR1-502 - Abstract
Hepatitis E virus (HEV) is an emerging public health issue in industrialized countries. In the last decade the number of autochthonous human infections has increased in Europe. Genotype 3 (HEV-3) is typically zoonotic, being foodborne the main route of transmission to humans, and is the most frequently detected in Europe in both humans and animals (mainly pigs and wild boars). In Italy, the first autochthonous human case was reported in 1999; since then, HEV-3 has been widely detected in both humans and animals. Despite the zoonotic characteristic of HEV-3 is well established, the correlation between animal and human strains has been poorly investigated in Italy. In the present study, we compared the subtype distribution of HEV-3 in humans and animals (swine and wild boar) in the period 2000–2018 from Italy. The dataset for this analysis included a total of 96 Italian ORF2 sequences (300 nt long), including both NCBI database-derived (n = 64) and recent sequences (2016–2018, n = 32) obtained in this study. The results show that subtype 3f is the most frequent in humans and pigs, followed by the HEV-3e, HEV-3c and other unassignable HEV-3 strains. Diversely, in wild boar a wider group of HEV-3 subtypes have been detected, including HEV-3a, which has also been detected for the first time in a human patient in Central Italy in 2017, and a wide group of unassignable HEV-3 strains. The phylogenetic analysis including, besides Italian strains, also sequences from other countries retrieved from the NCBI database, indicated that human Italian sequences, in particular those of HEV-3f and HEV-3e, form significant clusters mainly with sequences of animal origin from the same country. Nevertheless, for HEV-3c, rarely detected in Italian pigs, human sequences from Italy are more correlated to human sequences from other European countries. Furthermore, clusters of near-identical human strains identified in a short time interval in Lazio Region (Central Italy) can be recognized in the phylogenetic tree, suggesting that multiple infections originating from a common source have occurred, and confirming the importance of sequencing support to HEV surveillance.
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- 2020
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21. Torque Teno Sus Virus (TTSuV) Prevalence in Wild Fauna of Northern Italy
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Francesco Righi, Sara Arnaboldi, Virginia Filipello, Giovanni Ianiro, Ilaria Di Bartolo, Stefania Calò, Silvia Bellini, Tiziana Trogu, Davide Lelli, Alessandro Bianchi, Silvia Bonardi, Enrico Pavoni, Barbara Bertasi, and Antonio Lavazza
- Subjects
swine-related virus ,wild ungulates ,reservoir ,Biology (General) ,QH301-705.5 - Abstract
Torque teno sus virus (TTSuV) is a non-enveloped circular ssDNA virus which frequently infects swine and has been associated with hepatic, respiratory, and autoimmune disorders. TTSuV’s pathogenic role is still uncertain, and clear data in the literature on virus reservoirs are lacking. The aims of this study were to investigate the presence of potentially zoonotic TTSuV in wild animals in Northern Italy and to evaluate their role as reservoirs. Liver samples were collected between 2016 and 2020 during four hunting seasons from wild boars (Sus scrofa), red deer (Cervus elaphus), roe deer (Capreolus capreolus), and chamois (Rupicapra rupicapra). Samples originated from areas in Northern Italy characterized by different traits, i.e., mountains and flatland with, respectively low and high farm density and anthropization. Viral identification was carried out by end-point PCR with specific primers for TTSuV1a and TTSuVk2a species. TTSuV prevalence in wild boars was higher in the mountains than in the flatland (prevalence of 6.2% and 2.3%, respectively). In wild ruminants only TTSuVk2a was detected (with a prevalence of 9.4%). Our findings shed light on the occurrence and distribution of TTSuV in some wild animal species, investigating their possible role as reservoirs.
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- 2022
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22. Hepatitis E Virus Occurrence in Pigs Slaughtered in Italy
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Eleonora Chelli, Elisabetta Suffredini, Paola De Santis, Dario De Medici, Santina Di Bella, Stefania D’Amato, Francesca Gucciardi, Annalisa Guercio, Fabio Ostanello, Vitantonio Perrone, Giuseppa Purpari, Gaia Sofia Scavia, Pietro Schembri, Bianca Maria Varcasia, and Ilaria Di Bartolo
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hepatitis E virus ,pigs ,zoonosis ,genotype 3 ,slaughterhouse ,abattoir ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
In Europe, foodborne transmission has been clearly associated to sporadic cases and small clusters of hepatitis E in humans linked to the consumption of contaminated pig liver sausages, raw venison, or undercooked wild boar meat. In Europe, zoonotic HEV-genotype 3 strains are widespread in pig farms but little information is available on the prevalence of HEV positive pigs at slaughterhouse. In the present study, the prevalence of HEV-RNA positive pigs was assessed on 585 animals from 4 abattoirs located across Italy. Twenty-one pigs (3.6%) tested positive for HEV in either feces or liver by real-time RT-PCR. In these 21 pigs, eight diaphragm muscles resulted positive for HEV-RNA. Among animals collected in one abattoir, 4 out of 91 plasma tested positive for HEV-RNA. ELISA tests for the detection of total antibodies against HEV showed a high seroprevalence (76.8%), confirming the frequent exposure of pigs to the virus. The phylogenetic analyses conducted on sequences of both ORF1 and ORF2 fragments, shows the circulation of HEV-3c and of a novel unclassified subtype. This study provides information on HEV occurrence in pigs at the slaughterhouse, confirming that muscles are rarely contaminated by HEV-RNA compared to liver, which is the most frequently positive for HEV.
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- 2021
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23. Can Coronaviruses Steal Genes from the Host as Evidenced in Western European Hedgehogs by EriCoV Genetic Characterization?
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Luca De Sabato, Ilaria Di Bartolo, Maria Alessandra De Marco, Ana Moreno, Davide Lelli, Claudia Cotti, Mauro Delogu, and Gabriele Vaccari
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Erinaceus europaeus ,hedgehogs ,betacoronaviruses ,Erinaceus coronavirus ,EriCoV ,CD200 glycoprotein ,Microbiology ,QR1-502 - Abstract
Due to their need for living cells, viruses have developed adaptive evolutionary strategies to survive and perpetuate in reservoir hosts that play a crucial role in the ecology of emerging pathogens. Pathogenic and potentially pandemic betacoronaviruses arose in humans in 2002 (SARS-CoV, disappeared in July 2003), 2012 (MERS-CoV, still circulating in Middle East areas), and 2019 (SARS-CoV-2, causing the current global pandemic). As universally recognized, bats host ancestors of the above-mentioned zoonotic viruses. However, hedgehogs have been recently identified in Europe and Asia as possible reservoirs of MERS-CoV-like strains classified as Erinaceus coronavirus (EriCoV). To elucidate the evolution and genetics of EriCoVs, NGS (next generation sequencing) and Sanger sequencing were used to examine fecal samples collected in Northern Italy in 2018/2019 from 12 hedgehogs previously found EriCoV-positive by RT-PCR. By sequence analysis, eight complete EriCoV genomes, obtained by NGS, showed a high phylogenetic correlation with EriCoV strains previously reported in Eurasia. Interestingly, eight viral strains presented an additional ORF encoding for the CD200 ortholog located between the genes encoding for the Spike and the ORF3a proteins. The CD200 ortholog sequences were closely similar to the host CD200 protein but varying among EriCoVs. The result, confirmed by Sanger sequencing, demonstrates for the first time that CoVs can acquire host genes potentially involved in the immune-modulatory cascade and possibly enabling the virus to escape the host defence.
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- 2020
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24. Pilot Investigation on the Presence of Anti-Hepatitis E Virus (HEV) Antibodies in Piglet Processing Fluids
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Ilaria Di Bartolo, Luca De Sabato, Eleonora Chelli, Giovanni Loris Alborali, Matteo Tonni, Marina Monini, Alessia De Lucia, and Fabio Ostanello
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Hepatitis E virus ,serology ,swine ,surveillance ,processing fluids ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
Identifying Hepatitis E virus (HEV)-positive pig farms is important to implement surveillance programs for this emerging zoonotic agent. The aim of this study was to evaluate the use of serosanguineous fluids obtained as part of castration practice (processing fluids (PFs)) to detect anti-HEV antibodies in newborn piglets. Ninety-five paired serum and PF samples were collected from piglets of 29 different litters and tested with a commercial ELISA kit. A significant positive correlation (Spearman’s rho: 0.600; p < 0.01) was found between anti-HEV antibodies in serum and PF samples. In 26 out of 29 litters (89.7%), there was at least one positive piglet in the serum. Sixteen litters out of 29 (55.2%) were also positive in PFs. To simulate the use of PF as pooled samples, the limit of detection of the ELISA was assessed mixing the PF sample with strong, medium, medium-weak and weak ELISA titres with 3, 4, 5 and 6 negative PF samples. Our results suggest that it is still possible to identify a positive PF pool when at least one individual PF sample with medium or strong antibody levels is mixed with 5 or 6 individual negative PF samples. The detection of anti-HEV maternal-derived antibodies in PF confirms a past exposure of sows to the virus. PF may represent a rapid, noninvasive and economical tool to identify HEV-positive farms.
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- 2020
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25. Seroprevalence of Hepatitis E Virus in Forestry Workers from Trentino-Alto Adige Region (Northern Italy)
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Marina Monini, Fabio Ostanello, Alessandra Dominicis, Valentina Tagliapietra, Gabriele Vaccari, Annapaola Rizzoli, Claudia M. Trombetta, Emanuele Montomoli, and Ilaria Di Bartolo
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hepatitis E virus ,anti-HEV IgG seroprevalence ,forestry workers ,occupational risk ,Medicine - Abstract
People with some occupational or recreational activities, such as hunters and veterinarians, may have increased risk to be infected by the hepatitis E virus (HEV). The aim of the present study was to establish whether forestry workers could be considered at a higher risk of HEV infection than a control group. One hundred and fifty sera from forestry workers and a control group of 85 sera were analysed by anti-HEV IgG antibodies detection using a commercial ELISA kit. The anti-HEV IgG seroprevalence was 14% for forestry workers and 9.4% for the control group. Comparing the risk of HEV infection in the two groups, there was no difference in the odds ratio. However, the seroprevalence in older subjects was higher in the forestry workers than in the control group. Two sera from forestry workers were also positive for anti-HEV IgM, and, in one of them, HEV-RNA was detected. Our findings showed an increase of seroprevalence with age, which is likely to reflect cumulative exposure to HEV over time. The occupation of forestry workers did not seem to be associated with a higher risk of HEV infection. The study provided new insights into the risk of acquiring HEV in occupational exposure workers with open-air activities.
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- 2020
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26. Detection and Characterization of Porcine Sapelovirus in Italian Pig Farms
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Eleonora Chelli, Luca De Sabato, Gabriele Vaccari, Fabio Ostanello, and Ilaria Di Bartolo
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porcine sapelovirus ,swine ,PSV ,Italy ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
Porcine sapelovirus (PSV) belongs to the genus Sapelovirus of the family Picornaviridae. PSV infects pigs asymptomatically, but it can also cause severe neurologic, enteric, and respiratory symptoms or reproductive failure. Sapelovirus infections have been reported worldwide in pigs. The objective of this study was to investigate the presence and the prevalence of PSV in Italian swine farms in animals of different ages to clarify the occurrence of the infection and the genetic characteristics of circulating strains. In the present study, 92 pools of fecal samples, collected from pigs across three farms, were analyzed by Reverse Transcriptase-polymerase Chain Reaction-PCR (RT-PCR). Fecal pools from young growers (63/64) were found positive for Sapelovirus in all farms while detection in sows (4/28) was observed in only one farm. Phylogenetic analyses of the 19 partial capsid protein nucleotide sequences (VP1) (6–7 each farm) enable the classification of the virus sequences into three distinct clades and highlighted the high heterogeneity within one farm. The whole genome sequence obtained from one strain showed the highest correlation with the Italian strain detected in 2015. The study adds novel information about the circulation and heterogeneity of PSV strains in Italy and considering the movement of pigs across Europe would also be informative for other countries.
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- 2020
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27. Public health risks associated with hepatitis E virus (HEV) as a food‐borne pathogen
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EFSA Panel on Biological Hazards (BIOHAZ), Antonia Ricci, Ana Allende, Declan Bolton, Marianne Chemaly, Robert Davies, Pablo Salvador Fernandez Escamez, Lieve Herman, Kostas Koutsoumanis, Roland Lindqvist, Birgit Nørrung, Lucy Robertson, Giuseppe Ru, Moez Sanaa, Marion Simmons, Panagiotis Skandamis, Emma Snary, Niko Speybroeck, Benno Ter Kuile, John Threlfall, Helene Wahlström, Ilaria Di Bartolo, Reimar Johne, Nicole Pavio, Saskia Rutjes, Wim vander Poel, Petra Vasickova, Michaela Hempen, Winy Messens, Valentina Rizzi, Francesca Latronico, and Rosina Girones
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hepatitis E virus ,food‐borne ,pork ,wild boar ,liver ,HEV ,Nutrition. Foods and food supply ,TX341-641 ,Chemical technology ,TP1-1185 - Abstract
Abstract Hepatitis E virus (HEV) is an important infection in humans in EU/EEA countries, and over the last 10 years more than 21,000 acute clinical cases with 28 fatalities have been notified with an overall 10‐fold increase in reported HEV cases; the majority (80%) of cases were reported from France, Germany and the UK. However, as infection in humans is not notifiable in all Member States, and surveillance differs between countries, the number of reported cases is not comparable and the true number of cases would probably be higher. Food‐borne transmission of HEV appears to be a major route in Europe; pigs and wild boars are the main source of HEV. Outbreaks and sporadic cases have been identified in immune‐competent persons as well as in recognised risk groups such as those with pre‐existing liver damage, immunosuppressive illness or receiving immunosuppressive treatments. The opinion reviews current methods for the detection, identification, characterisation and tracing of HEV in food‐producing animals and foods, reviews literature on HEV reservoirs and food‐borne pathways, examines information on the epidemiology of HEV and its occurrence and persistence in foods, and investigates possible control measures along the food chain. Presently, the only efficient control option for HEV infection from consumption of meat, liver and products derived from animal reservoirs is sufficient heat treatment. The development of validated quantitative and qualitative detection methods, including infectivity assays and consensus molecular typing protocols, is required for the development of quantitative microbial risk assessments and efficient control measures. More research on the epidemiology and control of HEV in pig herds is required in order to minimise the proportion of pigs that remain viraemic or carry high levels of virus in intestinal contents at the time of slaughter. Consumption of raw pig, wild boar and deer meat products should be avoided.
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- 2017
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28. Hepatitis E Virus in Pork Production Chain in Czech Republic, Italy, and Spain, 2010
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Ilaria Di Bartolo, Marta Diez-Valcarce, Petra Vasickova, Petr Kralik, Marta Hernandez, Giorgia Angeloni, Fabio Ostanello, Martijn Bouwknegt, David Rodríguez-Lázaro, Ivo Pavlik, and Franco Maria Ruggeri
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Hepatitis E virus ,swine ,pork food chain ,molecular detection ,reverse transcriptase polymerase chain reaction ,zoonoses ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
We evaluated the prevalence of hepatitis E virus (HEV) in the pork production chain in Czech Republic, Italy, and Spain during 2010. A total of 337 fecal, liver, and meat samples from animals at slaughterhouses were tested for HEV by real-time quantitative PCR. Overall, HEV was higher in Italy (53%) and Spain (39%) than in Czech Republic (7.5%). HEV was detected most frequently in feces in Italy (41%) and Spain (39%) and in liver (5%) and meat (2.5%) in Czech Republic. Of 313 sausages sampled at processing and point of sale, HEV was detected only in Spain (6%). HEV sequencing confirmed only g3 HEV strains. Indicator virus (porcine adenovirus) was ubiquitous in fecal samples and absent in liver samples and was detected in 1 slaughterhouse meat sample. At point of sale, we found porcine adenovirus in sausages (1%–2%). The possible dissemination of HEV and other fecal viruses through pork production demands containment measures.
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- 2012
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29. Norovirus circulation in pediatric patients
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Sara Giordana Rimoldi, Cristina Pagani, Fabrizio Stefani, Nadia Zanchetta, Gian Vincenzo Zuccotti, Ilaria di Bartolo, Franco Ruggeri, and Maria Rita Gismondo
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Norovirus, sequencing, circulating strands, paediatric patients ,Microbiology ,QR1-502 - Abstract
An eighteen-month study (2008-2009) was carried out on patients, aged on average 30 months, admitted with gastroenteritis to the Paediatric Unit of the L. Sacco Hospital in Milan, Italy. Faecal samples of 154 patients were investigated for Rotavirus, Norovirus,Adenovirus, Enterovirus and Bocavirus. A total of 25 norovirus positive samples were selected for nucleotide sequence analysis, that allowed identify GII.2, GII.3 and GII.4 2006 virus variants (06 a, 06 b).
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- 2010
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30. Nosocomial outbreak of norovirus gastroenteritidis with unusual clinical-epidemiological features
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Marco Arosio, Annalisa Grigis, Enrico Castellucci, Giancarla Caglioni, Franca Averara, Francesco Locati, Barbara Marziali, Ilaria Di Bartolo, Franco Maria Ruggeri, and Antonio Goglio
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Norovirus, Gastroenteritis, Nosocomial outbreak. ,Microbiology ,QR1-502 - Abstract
Literature reports about Norovirus outbreaks, especially in hospitals, have accumulated in the past years, including patients and health workers.This report describes a small outbreak by Norovirus which occurred in USC Urology with unusual clinical-epidemiological features.The clinical course was unusual, as it presented no vomiting and duration of diarrhoea was unusually long (4-6 days) with the lack of involvement of health workers.The search for the virus was done with immunoassay method RIDASCREEN 2a generation on 11/19 patients (58%) with gastroenteritis symptoms, and 3/11 samples (27%) were positive. The molecular investigation by RT/PCR with diagnostic primers JV12 and JV13 on the polymerase region, carried out at the Istituto Superiore di Sanità, Rome, gave negative results while the RT/PCR using primers GIISKR and GIISKF, which amplify a fragment of the capsid region, was positive in 4/11 samples (36%) showing a correlation of 2/4 samples (50%) with RIDASCREEN immunoassay test. Our observations confirm the usefulness of immunoassay tests and the need to extend the molecular methods using different diagnostic primers. In outbreaks of gastroenteritis the microbiologist should consider the detection of Norovirus in diagnostic routine, as a positive result requires prevention measures to avoid also the spreading by droplets when vomiting is present.
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- 2008
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31. Long‐term surveillance for hepatitis E virus in an Italian two‐site farrow‐to‐finish swine farm
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Giovanni Ianiro, E. Chelli, Ilaria Di Bartolo, Marina Monini, Luca De Sabato, Fabio Ostanello, Ianiro, Giovanni, Chelli, Eleonora, De Sabato, Luca, Monini, Marina, Ostanello, Fabio, and Di Bartolo, Ilaria
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pig ,0301 basic medicine ,Veterinary medicine ,Farms ,Time Factors ,Swine ,Epidemiology ,viruses ,030231 tropical medicine ,030106 microbiology ,medicine.disease_cause ,Viral Zoonoses ,Virus ,Persistence (computer science) ,Feces ,03 medical and health sciences ,0302 clinical medicine ,Wild boar ,Hepatitis E virus ,biology.animal ,Genotype ,medicine ,Animals ,Phylogeny ,Swine Diseases ,Hepatitis ,General Veterinary ,General Immunology and Microbiology ,biology ,Transmission (medicine) ,Zoonosis ,Public Health, Environmental and Occupational Health ,virus diseases ,medicine.disease ,zoonosis ,digestive system diseases ,Hepatitis E ,Infectious Diseases ,HEV-3 ,Italy ,Population Surveillance ,surveillance ,farrow-to-finish farm - Abstract
In humans, hepatitis E virus (HEV) is responsible for an acute enterically transmitted hepatitis, which can become chronic in immune-compromised patients. Genotypes 3 and 4 (HEV-3 and HEV-4) are zoonotic, and domestic pigs and wild boar are the main reservoirs. The occurrence of autochthonous cases in Europe, which have been increasing over the last 10 years, has been associated with food-borne zoonotic transmission of HEV-3, mainly linked to consumption of undercooked or raw pork products (sausages containing liver) and wild boar meat. Zoonotic HEV-3 strains are widespread on pig farms, but little information is available on the dynamic of HEV-3 infection within farms, among pigs. The aims of this study were to evaluate the prevalence of the infection among pigs of different ages along the production chain by the zoonotic HEVs, and to evaluate how long the virus may persist in the farm environment. The presence of HEV-RNA was investigated by real-time reverse transcription PCR (RT-PCR) in 281 test faecal pools over 19 months (2017-2019) on a two-site farrow-to-finish farm (about 1,000 sows), in Northern Italy. A total of 67/281 test faecal pools (23.8%) resulted positive for the presence of HEV-RNA (site 1: 59/221, 26.7%; site 2: 8/60, 13.3%). Nucleotide sequencing revealed a unique HEV-3 viral variant circulating during 19 months of surveillance. The same HEV-3 strain was detected in the same farm on 2012, indicating the persistence of the same virus over 7 years, and highlighting the role of the environment as a continuous source of infection on pig farms. The results confirmed the circulation of the zoonotic genotype HEV-3 in pigs before slaughtering.
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- 2021
32. Novel subtypes and unexpected heterogeneity of hepatitis E viral strains in wild boar captured in a small area in Central Italy
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Luca De Sabato, Elisabetta Suffredini, Simona Di Pasquale, Giuseppina La Rosa, Paola De Santis, Monica Giammarioli, Gabriele Vaccari, and Ilaria Di Bartolo
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Swine Diseases ,Genotype ,General Veterinary ,General Immunology and Microbiology ,Swine ,viruses ,Sus scrofa ,virus diseases ,General Medicine ,digestive system diseases ,Hepatitis E ,Italy ,Hepatitis E virus ,Animals ,Humans ,RNA, Viral ,Phylogeny - Abstract
Wild boar is the main sylvatic reservoir of the genotype 3 of hepatitis E virus (HEV). The occurrence of HEV-3 human cases has been linked to the consumption of raw or undercooked pig and wild boar meat and liver. The zoonotic transmission of HEV-3 has been confirmed by sequencing identical or strictly related viral strains in humans, wild boar, and derived food. The HEV sequences classified within the HEV-3 genotype are highly variable, and although only one serotype has been identified so far, the observed differences allow for the further classification of the HEV-3 genotype into subtypes, named in alphabetical order. Compared to human and pig strains, an even higher heterogeneity is observed among strains infecting wild boar. In the present study, the genetic variability of eight HEV-3 strains detected in wild boars living in a small geographical area in central Italy (Lazio and Umbria regions) was investigated by full genome sequencing and phylogenetic analysis. The strains were classified within the HEV-3a, HEV-3c, HEV-3f subtypes and within two new recently proposed subtypes. Results demonstrate – despite the relatively small geographic area of origin – an unexpected divergence within HEV-3 strains hosted by the investigated wild boar population and highlights the need for extensive sequencing of HEV in reservoirs to fully understand diversity, geographical distribution and evolution of this group of viruses.
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- 2022
33. Detection of antibodies against influenza D virus in swine veterinarians in Italy in 2004
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Chiara Chiapponi, Serena Marchi, Fabio Ostanello, Claudia Maria Trombetta, Ilaria Di Bartolo, Emanuele Montomoli, Trombetta, Claudia Maria, Montomoli, Emanuele, Di Bartolo, Ilaria, Ostanello, Fabio, Chiapponi, Chiara, and Marchi, Serena
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Swine ,veterinarians ,Biology ,Antibodies, Viral ,Virus ,Serology ,Haemagglutination inhibition assay ,Orthomyxoviridae Infections ,Seroepidemiologic Studies ,Virology ,Seroprevalence ,Animals ,Humans ,Italy ,influenza D viruses ,Natural reservoir ,Swine Diseases ,influenza D viruse ,Serum samples ,biology.organism_classification ,Orthomyxoviridae ,Infectious Diseases ,biology.protein ,Cattle ,Antibody ,Thogotovirus - Abstract
Influenza D virus was firstly isolated from a swine with respiratory disease symptoms in 2011 in USA. Epidemiological and serological studies support the hypothesis that cattle represent the natural reservoir of influenza D virus with periodical spillover events to other animal hosts. Little is known about the seroprevalence in humans and in specific target groups such as veterinarians in Italy. This study was designed to assess the prevalence of antibodies against two influenza D lineages (D/660 and D/OK) in Italy in archived serum samples from veterinarians working with swine collected in 2004. Serum samples were tested by haemagglutination inhibition and virus neutralization assays. Results showed that 4.88% (4/82) of tested samples were positive for D/660 and 2.44% (2/82) for D/OK by haemagglutination inhibition assay. Three out of 4 samples showed positivity when tested by virus neutralization assay. Our data suggest undetected influenza D viruses might have circulated and/or introduced in Italy as early as 2004 at least in some animal species such as swine. In addition, it seems that the virus was circulating among veterinarians before the first isolation in 2011. This finding highlights the importance to continue monitoring influenza D virus spread in animals and humans for a more detailed surveillance. This article is protected by copyright. All rights reserved.
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- 2022
34. In Vitro Replication of Swine Hepatitis E Virus (HEV): Production of Cell-Adapted Strains
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Gabriele Vaccari, Fabio Ostanello, Ilaria Di Bartolo, Giovanni Ianiro, Marina Monini, Luca De Sabato, and Maria Grazia Ammendolia
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General Veterinary ,HEV ,subtype ,HEV-3 ,A549 ,isolate ,cell culture ,ORF2 ,swine ,zoonosis ,Animal Science and Zoology - Abstract
The hepatitis E caused by the virus HEV of genotypes HEV-3 and HEV-4 is a zoonotic foodborne disease spread worldwide. HEV is currently classified into eight different genotypes (HEV-1–8). Genotypes HEV-3 and HEV-4 are zoonotic and are further divided into subtypes. Most of the information on HEV replication remains unknown due to the lack of an efficient cell cultivation system. Over the last couple of years, several protocols for HEV cultivation have been developed on different cell lines; even if they were troublesome, long, and scarcely reproducible, they offered the opportunity to study the replicative cycle of the virus. In the present study, we aimed to obtain a protocol ready to use viral stock in serum free medium that can be used with reduced time of growth and without any purification steps. The employed method allowed isolation and cell adaptation of four swine HEV-3 strains, belonging to three different subtypes. Phylogenetic analyses conducted on partial genome sequences of in vitro isolated strains did not reveal any insertion in the hypervariable region (HVR) of the genomes. A limited number of mutations was acquired in the genome during the virus growth in the partial sequences of Methyltransferase (Met) and ORF2 coding genes.
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- 2023
35. Ricerca del virus dell’epatite E (HEV) nei cinghiali nella Tenuta Presidenziale di Castelporziano
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ILARIA DI BARTOLO, BARBARA FRANZETTI, DANIELE CECCA, GIULIA BONELLA, MARCO APOLLONIO, FABIO OSTANELLO, AA.VV., and ILARIA DI BARTOLO, BARBARA FRANZETTI, DANIELE CECCA, GIULIA BONELLA, MARCO APOLLONIO, FABIO OSTANELLO
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Wild Boar, Hepatitis E Virus, Zoonoses, Virus - Abstract
Nell’uomo, il virus dell’epatite E (HEV) è la causa più comune di epatite virale acuta, responsabile su scala globale di circa 20 milioni di casi ogni anno, di cui 70.000 letali. HEV, in particolare i due genotipi esclusivamente umani HEV-1 e HEV-2, è endemico in molti Paesi in via di sviluppo. Nei Paesi industrializzati, negli ultimi 10 anni, si è osservato un aumento del numero di casi di epatite E in pazienti senza anamnesi di viaggi in aree endemiche, sostenuti dai genotipi zoonotici HEV-3 e HEV-4. Queste infezioni sono in genere asintomatiche ma, in un numero ridotto di soggetti, possono evolvere in forme di epatite acuta. Ceppi di HEV-3 e HEV-4 sono stati identificati nei suini domestici, nei cinghiali, nei cervi e nei conigli. In queste specie l’infezione è asintomatica e si trasmette all’uomo principalmente per via alimentare mediante prodotti a base di carne, consumati crudi o poco cotti (salsicce contenenti fegato di suino o carne di cinghiale, sashimi di cervo). La presenza del genotipo zoonotico HEV-3 è stata segnalata in numerose popolazioni di cinghiale in tutta Europa. In Italia, numerosi studi ne hanno segnalato la presenza in popolazioni di cinghiale di quasi tutte le Regioni con prevalenze variabili tra 1,8% e 52%. Ad oggi, non è chiaro se l’infezione abbia avuto un’origine comune nelle popolazioni di suini domestici e selvatici o se l’infezione abbia iniziato a circolare nel selvatico a seguito di contatti con suini domestici (allevamento brado, immissioni a scopo venatorio di capi selvatici allevati in modo promiscuo). Il presente lavoro ha avuto lo scopo di indagare la presenza di HEV nella popolazione di cinghiali della Tenuta Presidenziale di Castelporziano. Questa popolazione ha la peculiare caratteristica di essere composta esclusivamente da cinghiali autoctoni e di non avere avuto contatti con altre popolazioni animali esterne alla Tenuta negli ultimi quarant’anni. Durante i mesi di novembre-gennaio del 2017-2020 sono stati prelevati 115 fegati da altrettanti cinghiali abbattuti nell’ambito dei piani di controllo condotti nella Tenuta e finalizzati alla conservazione della biodiversità protetta nell’area e al suo mantenimento in equilibrio. Porzioni di fegato, organo all’interno del quale avviene la replicazione del virus, sono state utilizzate per la ricerca dell’RNA di HEV mediante il metodo molecolare della Real-Time RT-PCR. Le analisi hanno rilevato la presenza del materiale genetico del virus in 2 dei 115 campioni analizzati. La prevalenza rilevata è estremamente bassa (1,7%) e nettamente inferiore a quella presente in altre popolazioni di cinghiale. Ciò potrebbe suggerire una possibile recente introduzione del virus all’interno della Tenuta con un rischio estremamente ridotto di contaminazione delle carcasse. In conclusione questo risultato porta a ritenere che l’isolamento degli animali o la loro densità possa essere importante nel determinare la diffusione del virus nelle popolazioni di cinghiale. Monitoring of hepatitis E virus (HEV in wild boar population within the Tenuta Presidenziale of Castelporziano. In humans, hepatitis E virus (HEV) is a common cause of acute viral hepatitis. The HEV is endemic in many developing countries. In Europe, in the last 10 years there has been an increase in cases of autochthonous hepatitis E, linked to zoonotic genotypes 3 and 4 (HEV-3 and HEV-4), which may cause asymptomatic infections that may evolve into acute hepatitis. The HEV-3 and HEV-4 have been identified in domestic pigs, wild boars, deer and rabbits. In these species, the infection is asymptomatic and is transmitted to humans mainly by consumption of raw or undercooked food (sausages containing pork liver or wild boar meat, deer sashimi). Wild boar is susceptible to the infection and animals positive for the HEV-3 zoonotic genotype have also been identified throughout Italy, in almost all Regions with prevalence varying between 1.8% and 52%. It is unclear whether the infection had a common origin in domestic and feral pig populations. The present work aims to investigate the presence of the virus in the wild boar population present within the Tenuta Presidenziale of Castelporziano, which has remained isolated over the last forty years. During November-January 2017-2020, 115 livers were taken from wild boars killed as part of the control plans for protection of biodiversity. Liver samples, the organ of viral replication, were used for the detection of Hepatitis E virus RNA by using the molecular method of Real-Time RT-PCR. Results revealed the presence of the genetic material of the virus in 2 of the 115 animals analyzed. The prevalence found is extremely low (1.7%) and significantly lower than that found in other wild boar populations. This could suggest a possible recent introduction of the virus inside the Tenuta. In conclusion, this result leads us to believe that the isolation of animals may be important to prevent the spread of the virus in wild boar populations.
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- 2021
36. Accumulation and Depuration Kinetics of Rotavirus in Mussels Experimentally Contaminated
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Antonio Luca Langellotti, Giovanni Ianiro, Valeria Russo, Anna Martello, Ilaria Di Bartolo, Giovanna Fusco, Marina Monini, Denise Di Concilio, Giorgio Galiero, Maria Grazia Amoroso, Amoroso, M. G., Langellotti, A. L., Russo, V., Martello, A., Monini, M., Di Bartolo, I., Ianiro, G., Di Concilio, D., Galiero, G., and Fusco, G.
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Rotavirus ,0301 basic medicine ,Epidemiology ,Health, Toxicology and Mutagenesis ,Microorganism ,030106 microbiology ,Mytilu ,Food Contamination ,010501 environmental sciences ,medicine.disease_cause ,01 natural sciences ,Virus ,03 medical and health sciences ,Virology ,medicine ,Animals ,Food science ,Shellfish ,0105 earth and related environmental sciences ,Kinetic ,Mytilus ,Infectivity ,biology ,Animal ,Chemistry ,Contamination ,Rotaviru ,biology.organism_classification ,Bioaccumulation ,Kinetics ,Mussel ,Depuration ,Bacteria ,Food Science - Abstract
Bivalve mollusks as filter-feeders concentrate in their digestive tissue microorganisms likely present in the harvesting water, thus becoming risky food especially if consumed raw or poorly cooked. To eliminate bacteria and viruses eventually accumulated, they must undergo a depuration process which efficacy on viruses is on debate. To better clarify the worth of the depuration process on virus elimination from mussels, in this study we investigated rotavirus kinetics of accumulation and depuration in Mytilus galloprovincialis experimentally contaminated. Depuration process was monitored for 9 days and virus residual presence and infectivity were evaluated by real time quantitative polymerase chain reaction, cell culture and electron microscopy at days 1, 2, 3, 5, 7, 9 of depuration. Variables like presence of ozone and of microalgae feeding were also analyzed as possible depuration enhancers. Results showed a two-phase virus removal kinetic with a high decrease in the first 24 h of depuration and 5 days necessary to completely remove rotavirus.
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- 2019
37. Detection of hepatitis E virus RNA in rats caught in pig farms from Northern Italy
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Fabio Ostanello, Alessia De Lucia, Marina Monini, Ilaria Di Bartolo, Luca De Sabato, Giovanni Ianiro, De Sabato, Luca, Ianiro, Giovanni, Monini, Marina, De Lucia, Alessia, Ostanello, Fabio, and Di Bartolo, Ilaria
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0301 basic medicine ,Swine ,Epidemiology ,viruses ,030106 microbiology ,030231 tropical medicine ,Orthohepevirus ,medicine.disease_cause ,Rodent Diseases ,03 medical and health sciences ,0302 clinical medicine ,Hepatitis E virus ,Wild boar ,Zoonoses ,biology.animal ,Genotype ,medicine ,Animals ,rat ,Orthohepevirus C ,Phylogeny ,mouse ,Disease Reservoirs ,Orthohepevirus A ,Swine Diseases ,2. Zero hunger ,General Veterinary ,General Immunology and Microbiology ,biology ,Transmission (medicine) ,Public Health, Environmental and Occupational Health ,virus diseases ,RNA ,Hepatitis E ,medicine.disease ,biology.organism_classification ,Virology ,digestive system diseases ,Rats ,3. Good health ,Infectious Diseases ,Italy ,RNA, Viral ,hepatitis E ,House mice ,hepatitis E viru - Abstract
Hepatitis E virus (HEV) strains belonging to the Orthohepevirus genus are divided into four species (A-D). HEV strains included in the Orthohepevirus A species infect humans and several other mammals. Among them, the HEV-3 and HEV-4 genotypes are zoonotic and infect both humans and animals, of which, pigs and wild boar are the main reservoirs. Viruses belonging to the Orthohepevirus C species (HEV-C) have been considered to infect rats of different species and carnivores. Recently, two studies reported the detection of HEV-C1 (rat HEV) RNA in immunocompromised and immunocompetent patients, suggesting a possible transmission of rat HEV to humans. The role of rats and mice as reservoir of HEV and the potential zoonotic transmission is still poorly known and deserves further investigation. To this purpose, in this study, the presence of HEV RNA was investigated in the intestinal contents and liver samples from 47 Black rats (Rattus rattus) and 21 House mice (Mus musculus) captured in four pig farms in Northern Italy. The presence of both Orthohepevirus A and C was investigated by the real-rime RT-PCR specific for HEV-1 to HEV-4 genotypes of Orthohepevirus A species and by a broad spectrum hemi-nested RT-PCR capable of detecting different HEV species including rat HEV. The intestinal content from two Black rats resulted positive for HEV-C1 RNA and for HEV-3 RNA, respectively. None of the House mice was HEV RNA positive. Sequence analyses confirmed the detection of HEV-C1, genotype G1 and HEV-3 subtype e. The viral strain HEV-3e detected in the rat was identical to swine HEV strains detected in the same farm. Liver samples were negative for the detection of either rat HEV or HEV-3.
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- 2019
38. Full genome characterization of two novel Alpha-coronavirus species from Italian bats
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Gabriele Vaccari, Davide Lelli, Ilaria Di Bartolo, Luca De Sabato, Ana Moreno, Sabrina Canziani, and Francesca Faccin
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Cancer Research ,viruses ,Sequence Homology ,Genome, Viral ,medicine.disease_cause ,Genome ,Article ,03 medical and health sciences ,Phylogenetics ,Chiroptera ,Virology ,Bats ,medicine ,Animals ,Pipistrellus kuhlii ,Pipistrellus ,Pipistrellus pipistrellus ,Phylogeny ,030304 developmental biology ,Coronavirus ,Genetics ,Whole genome sequencing ,0303 health sciences ,biology ,Phylogenetic tree ,030306 microbiology ,Computational Biology ,High-Throughput Nucleotide Sequencing ,virus diseases ,biochemical phenomena, metabolism, and nutrition ,respiratory system ,Alpha-CoV viruses ,biology.organism_classification ,Full genome sequencing ,respiratory tract diseases ,Infectious Diseases ,Italy ,Coronavirus Infections - Abstract
Highlights • Three Alpha-CoV strains were fully sequenced by NGS method. • The Italian strains were classified into two novel Alpha-CoV species. • The phylogenetic analysis on RdRp fragment sequences showed correlation to European strains., Coronaviruses (CoVs) have been detected worldwide in several bat species, which are considered the main reservoir. The attention to the high diversity of CoVs hosted by bats has increased during the last decade due to the high number of human infections caused by two zoonotic Beta-CoVs, SARS-CoV and MERS-CoV, that cause several respiratory diseases. Among coronaviruses, two Alpha-CoV strains (HuCoV-229E and HuCoV-NL63) cause mild respiratory disease that can change to severe disease in children, elderly and individuals affected by illnesses. Phylogenetic analysis conducted on bat Alpha-CoV strains revealed their evolutive correlation to human strains, suggesting their origin in bats. The genome of CoVs is characterized by a high frequency of mutations and recombination events, increasing their ability to switch hosts and their zoonotic potential. In this study, three strains of Alpha-CoV genera detected in Italian bats (Pipistrellus kuhlii) were fully sequenced by Next Generation Sequencing (NGS) and characterized. The complete genome analysis showed the correlation of the Italians strains with a Chinese strain detected in 2013 and, based on CoV molecular species demarcation, two new Alpha-CoV species were established. The analysis of a fragment of the RNA-dependent RNA polymerase (RdRp) showed the correlation of the Italian strains with CoVs that was only detected in the bat Pipistrellus genera (Pipistrellus kuhlii and Pipistrellus Pipistrellus) in European countries.
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- 2019
39. Detection and whole genome sequencing of murine norovirus in animal facility in Italy
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Giorgia Angeloni, Mauro Valeri, Silvia Tofani, Michele Angelo Di Bari, Giovanni Ianiro, Luca De Sabato, Claudia D'Agostino, Marina Monini, Ilaria Di Bartolo, and E. Ponterio
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0301 basic medicine ,viruses ,ved/biology.organism_classification_rank.species ,Bioengineering ,Biology ,Rodent Diseases ,03 medical and health sciences ,Mice ,Feces ,fluids and secretions ,stomatognathic system ,Family Caliciviridae ,Animals ,Caliciviridae Infections ,Whole genome sequencing ,Whole Genome Sequencing ,ved/biology ,Norovirus ,0402 animal and dairy science ,virus diseases ,04 agricultural and veterinary sciences ,Genus Norovirus ,Isolation (microbiology) ,040201 dairy & animal science ,Virology ,digestive system diseases ,Gastroenteritis ,030104 developmental biology ,Animal Science and Zoology ,Animal facility ,Biotechnology ,Murine norovirus - Abstract
Viruses belonging to the genus Norovirus (NoV) of the family Caliciviridae are the major cause of acute viral gastroenteritis worldwide. NoVs are classified into 10 genogroups (GI-GX), and those be...
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- 2021
40. SARS-CoV-2 RECoVERY: a multi-platform open-source bioinformatic pipeline for the automatic construction and analysis of SARS-CoV-2 genomes from NGS sequencing data
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Arnold Knijn, Luca De Sabato, Giovanni Ianiro, Gabriele Vaccari, Ilaria Di Bartolo, and Stefano Morabito
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Massive parallel sequencing ,Computer science ,Phylogenetics ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Interface (computing) ,medicine ,Computational biology ,medicine.disease_cause ,Genome ,Pipeline (software) ,DNA sequencing ,Coronavirus - Abstract
BackgroundSince its first appearance in December 2019, the novel Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), spread worldwide causing an increasing number of cases and deaths (35,537,491 and 1,042,798, respectively at the time of writing, https://covid19.who.int). Similarly, the number of complete viral genome sequences produced by Next Generation Sequencing (NGS), increased exponentially. NGS enables a rapid accumulation of a large number of sequences. However, bioinformatics analyses are critical and require combined approaches for data analysis, which can be challenging for non-bioinformaticians.ResultsA user-friendly and sequencing platform-independent bioinformatics pipeline, named SARS-CoV-2 RECoVERY (REconstruction of CoronaVirus gEnomes & Rapid analYsis) has been developed to build SARS-CoV-2 complete genomes from raw sequencing reads and to investigate variants. The genomes built by SARS-CoV-2 RECoVERY were compared with those obtained using other software available and revealed comparable or better performances of SARS–CoV2 RECoVERY. Depending on the number of reads, the complete genome reconstruction and variants analysis can be achieved in less than one hour. The pipeline was implemented in the multi-usage open-source Galaxy platform allowing an easy access to the software and providing computational and storage resources to the community.ConclusionsSARS-CoV-2 RECoVERY is a piece of software destined to the scientific community working on SARS-CoV-2 phylogeny and molecular characterisation, providing a performant tool for the complete reconstruction and variants’ analysis of the viral genome. Additionally, the simple software interface and the ability to use it through a Galaxy instance without the need to implement computing and storage infrastructures, make SARS-CoV-2 RECoVERY a resource also for virologists with little or no bioinformatics skills.Availability and implementationThe pipeline SARS-CoV-2 RECoVERY (REconstruction of COronaVirus gEnomes & Rapid analYsis) is implemented in the Galaxy instance ARIES (https://aries.iss.it).
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- 2021
41. Possible Human-to-Dog Transmission of SARS-CoV-2, Italy, 2020
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Gabriella Elia, Grant L. Hughes, Gabriele Vaccari, Sergio Rosati, Barbara Colitti, Costantina Desario, Alessio Lorusso, Cesare Cammà, Eleonora Lorusso, Nicola Decaro, Luca De Sabato, Umberto Agrimi, Vito Martella, Ilaria Di Bartolo, Liana Teodori, Dominga Ricci, Domenico Buonavoglia, and Edward I Patterson
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Microbiology (medical) ,2019-20 coronavirus outbreak ,dogs ,Epidemiology ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,viruses ,030231 tropical medicine ,coronavirus ,Infectious and parasitic diseases ,RC109-216 ,medicine.disease_cause ,phylogeny ,DNA sequencing ,2019 novel coronavirus disease ,03 medical and health sciences ,respiratory infections ,0302 clinical medicine ,medicine ,Research Letter ,Animals ,030212 general & internal medicine ,Seroconversion ,humans ,Coronavirus ,SARS-CoV-2 transmission ,biology ,Transmission (medicine) ,SARS-CoV-2 ,COVID-19 ,Serum samples ,Virology ,zoonoses ,Infectious Diseases ,Italy ,coronavirus disease ,biology.protein ,Medicine ,next-generation sequencing ,Antibody ,Possible Human-to-Dog Transmission of SARS-CoV-2, Italy, 2020 ,severe acute respiratory syndrome coronavirus 2 - Abstract
We detected severe acute respiratory syndrome coronavirus 2 in an otherwise healthy poodle living with 4 family members who had coronavirus disease. We observed antibodies in serum samples taken from the dog, indicating seroconversion. Full-length genome sequencing showed that the canine and human viruses were identical, suggesting human-to-animal transmission.
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- 2021
42. Hepatitis E Virus Occurrence in Pigs Slaughtered in Italy
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E. Chelli, Fabio Ostanello, Vitantonio Perrone, Pietro Schembri, Stefania D'Amato, Gaia Scavia, Ilaria Di Bartolo, Paola De Santis, Elisabetta Suffredini, Annalisa Guercio, Giuseppa Purpari, Bianca Maria Varcasia, Francesca Gucciardi, Dario De Medici, Santina Di Bella, Chelli, Eleonora, Suffredini, Elisabetta, De Santis, Paola, De Medici, Dario, Di Bella, Santina, D’Amato, Stefania, Gucciardi, Francesca, Guercio, Annalisa, Ostanello, Fabio, Perrone, Vitantonio, Purpari, Giuseppa, Scavia, Gaia Sofia, Schembri, Pietro, Varcasia, Bianca Maria, and Di Bartolo, Ilaria
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pig ,Veterinary medicine ,viruses ,abattoir ,hepatitis E virus ,medicine.disease_cause ,zoonosi ,Virus ,Article ,Wild boar ,Hepatitis E virus ,biology.animal ,lcsh:Zoology ,medicine ,Seroprevalence ,genotype 3 ,lcsh:QL1-991 ,Feces ,lcsh:Veterinary medicine ,General Veterinary ,biology ,Zoonosis ,pigs ,virus diseases ,zoonosis ,slaughterhouse ,Hepatitis E ,medicine.disease ,digestive system diseases ,Italy ,biology.protein ,lcsh:SF600-1100 ,Animal Science and Zoology ,Antibody ,hepatitis E viru - Abstract
Simple Summary Hepatitis E is now recognized as an emerging zoonotic disease in Europe caused by an RNA virus (HEV) and foodborne is the main route of transmission. Human cases have been linked to the consumption of contaminated pig liver sausages, raw venison, or undercooked wild boar meat. The zoonotic genotype HEV-3 is widespread in pigs at farm level but little information is available on the occurrence of HEV-positive pigs at the slaughterhouse. The aim of this study was to investigate the prevalence of HEV-positive pigs during slaughtering, to understand which biological samples (feces and organs) were more frequently HEV positive. Our results showed that pigs positive for HEV can be slaughtered and that the percentage of positive animals depends on the age of animals. The other main result is the presence of the virus in the plasma of animals, which may contribute to the contamination of meat (muscle). Nevertheless, muscles are rarely contaminated by HEV-RNA compared to liver, which is the organ of replication. Abstract In Europe, foodborne transmission has been clearly associated to sporadic cases and small clusters of hepatitis E in humans linked to the consumption of contaminated pig liver sausages, raw venison, or undercooked wild boar meat. In Europe, zoonotic HEV-genotype 3 strains are widespread in pig farms but little information is available on the prevalence of HEV positive pigs at slaughterhouse. In the present study, the prevalence of HEV-RNA positive pigs was assessed on 585 animals from 4 abattoirs located across Italy. Twenty-one pigs (3.6%) tested positive for HEV in either feces or liver by real-time RT-PCR. In these 21 pigs, eight diaphragm muscles resulted positive for HEV-RNA. Among animals collected in one abattoir, 4 out of 91 plasma tested positive for HEV-RNA. ELISA tests for the detection of total antibodies against HEV showed a high seroprevalence (76.8%), confirming the frequent exposure of pigs to the virus. The phylogenetic analyses conducted on sequences of both ORF1 and ORF2 fragments, shows the circulation of HEV-3c and of a novel unclassified subtype. This study provides information on HEV occurrence in pigs at the slaughterhouse, confirming that muscles are rarely contaminated by HEV-RNA compared to liver, which is the most frequently positive for HEV.
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- 2021
43. Molecular detection and phylogenetic analysis of HEV-3 in wild boars in Central Italy
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Luca De Sabato, Gabriele Vaccari, Fabio Ostanello, Luigi De Grossi, Marina Monini, Giovanni Ianiro, Ilaria Di Bartolo, and Luca De Sabato, Gabriele Vaccari, Fabio Ostanello, Luigi De Grossi, Marina Monini, Giovanni Ianiro, Ilaria Di Bartolo
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endocrine system ,HEV, wild boar, phylogenetic analysis ,urogenital system ,virus diseases - Abstract
Background: Hepatitis E virus (HEV) causes acute hepatitis in humans. Over the last decade, in Europe, the zoonotic HEV-3 genotype has caused an increasing number of autochthonous cases linked to the consumption of raw or undercooked pork products and wild boar meat. In Italy, HEV-3 is widespread in both pigs and wild boar. In this study, 207 wild boar hunted in central Italy were tested for HEV. Methods: Liver samples from 207 wild boars (Sus scrofa) were collected from 2016 to 2018. The HEV RNA was extracted from 100 milligrams of liver and detected by quantitative RT-qPCR. A 348-bp fragment within the ORF2 was amplified by nested RT-PCR. Full genome of 4 strains was obtained by NGS multiplex PCRs (Ion Personal Genome Machine). Results: HEV RNA was detected in 29.5% (61/207) of liver. The phylogenetic analysis conducted on short genomic sequences showed the circulation of -3f (n=2), -3c (n=5) subtype strains and two clusters of HEV-3* unclassified strains (n=18). Four strains were fully sequenced by NGS and classified into the -3f, -3c, -3i and one HEV-3*. The latter subtype forms a cluster with other European swine and human strains and was recently proposed. The sequenced strains were related (94-99% nt.id.) to wild boar, human and pig strains identified in Italy. Conclusion: In this study, a high heterogeneity of HEV-3 strains was revealed in wild boar. Strains are more correlated to other wild boar strains detected in Europe than to Italian pig strains. Only three wild boar strains were correlated (94% nt. id.) to an Italian human strain detected in a patient who declared consumption of figatelli (liver sausage) in 2011. Wild boar plays an important role as a source of infection of HEV-3 to breeding pig populations and to humans in those regions where wild boar meat is consumed frequently.
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- 2019
44. Pilot Investigation on the Presence of Anti-Hepatitis E Virus (HEV) Antibodies in Piglet Processing Fluids
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Fabio Ostanello, Giovanni Loris Alborali, Marina Monini, Luca De Sabato, Matteo Tonni, Alessia De Lucia, Ilaria Di Bartolo, E. Chelli, Di Bartolo, Ilaria, De Sabato, Luca, Chelli, Eleonora, Alborali, Giovanni Lori, Tonni, Matteo, Monini, Marina, De Lucia, Alessia, and Ostanello, Fabio
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040301 veterinary sciences ,serology ,Antibody level ,medicine.disease_cause ,Virus ,Article ,Serology ,0403 veterinary science ,03 medical and health sciences ,Elisa kit ,Hepatitis E virus ,lcsh:Zoology ,medicine ,Hepatitis E viru ,lcsh:QL1-991 ,processing fluids ,Pig farms ,030304 developmental biology ,0303 health sciences ,lcsh:Veterinary medicine ,General Veterinary ,biology ,swine ,04 agricultural and veterinary sciences ,Virology ,Significant positive correlation ,biology.protein ,surveillance ,lcsh:SF600-1100 ,Animal Science and Zoology ,Antibody - Abstract
Identifying Hepatitis E virus (HEV)-positive pig farms is important to implement surveillance programs for this emerging zoonotic agent. The aim of this study was to evaluate the use of serosanguineous fluids obtained as part of castration practice (processing fluids (PFs)) to detect anti-HEV antibodies in newborn piglets. Ninety-five paired serum and PF samples were collected from piglets of 29 different litters and tested with a commercial ELISA kit. A significant positive correlation (Spearman’s rho: 0.600, p <, 0.01) was found between anti-HEV antibodies in serum and PF samples. In 26 out of 29 litters (89.7%), there was at least one positive piglet in the serum. Sixteen litters out of 29 (55.2%) were also positive in PFs. To simulate the use of PF as pooled samples, the limit of detection of the ELISA was assessed mixing the PF sample with strong, medium, medium-weak and weak ELISA titres with 3, 4, 5 and 6 negative PF samples. Our results suggest that it is still possible to identify a positive PF pool when at least one individual PF sample with medium or strong antibody levels is mixed with 5 or 6 individual negative PF samples. The detection of anti-HEV maternal-derived antibodies in PF confirms a past exposure of sows to the virus. PF may represent a rapid, noninvasive and economical tool to identify HEV-positive farms.
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- 2020
45. Detection and Characterization of Porcine Sapelovirus in Italian Pig Farms
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Ilaria Di Bartolo, Gabriele Vaccari, Luca De Sabato, Fabio Ostanello, E. Chelli, Chelli, Eleonora, De Sabato, Luca, Vaccari, Gabriele, Ostanello, Fabio, and Di Bartolo, Ilaria
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Whole genome sequencing ,Veterinary medicine ,food.ingredient ,lcsh:Veterinary medicine ,General Veterinary ,Phylogenetic tree ,genetic structures ,porcine sapelovirus ,Strain (biology) ,swine ,Biology ,porcine sapeloviru ,Virus ,Article ,PSV ,food ,Italy ,lcsh:Zoology ,Porcine sapelovirus ,lcsh:SF600-1100 ,Animal Science and Zoology ,lcsh:QL1-991 ,Clade ,Feces ,Sapelovirus - Abstract
Porcine sapelovirus (PSV) belongs to the genus Sapelovirus of the family Picornaviridae. PSV infects pigs asymptomatically, but it can also cause severe neurologic, enteric, and respiratory symptoms or reproductive failure. Sapelovirus infections have been reported worldwide in pigs. The objective of this study was to investigate the presence and the prevalence of PSV in Italian swine farms in animals of different ages to clarify the occurrence of the infection and the genetic characteristics of circulating strains. In the present study, 92 pools of fecal samples, collected from pigs across three farms, were analyzed by Reverse Transcriptase-polymerase Chain Reaction-PCR (RT-PCR). Fecal pools from young growers (63/64) were found positive for Sapelovirus in all farms while detection in sows (4/28) was observed in only one farm. Phylogenetic analyses of the 19 partial capsid protein nucleotide sequences (VP1) (6&ndash, 7 each farm) enable the classification of the virus sequences into three distinct clades and highlighted the high heterogeneity within one farm. The whole genome sequence obtained from one strain showed the highest correlation with the Italian strain detected in 2015. The study adds novel information about the circulation and heterogeneity of PSV strains in Italy and considering the movement of pigs across Europe would also be informative for other countries.
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- 2020
46. Can Coronaviruses Steal Genes from the Host as Evidenced in Western European Hedgehogs by EriCoV Genetic Characterization?
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Ana Moreno, Gabriele Vaccari, Ilaria Di Bartolo, Mauro Delogu, Luca De Sabato, Davide Lelli, Maria Alessandra De Marco, Claudia Cotti, De Sabato L., Di Bartolo I., De Marco M.A., Moreno A., Lelli D., Cotti C., Delogu M., and Vaccari G.
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0301 basic medicine ,CD200 glycoprotein ,viruses ,lcsh:QR1-502 ,medicine.disease_cause ,Genome ,lcsh:Microbiology ,Betacoronavirus infection ,Chiroptera ,EriCoV ,Erinaceus europaeus ,Phylogeny ,Coronavirus ,Genetics ,Sanger sequencing ,Base Composition ,Erinaceus ,biology ,Erinaceus coronavirus ,betacoronaviruse ,Erinaceus coronaviru ,Infectious Diseases ,Spike Glycoprotein, Coronavirus ,Middle East Respiratory Syndrome Coronavirus ,symbols ,Erinaceus europaeu ,Coronavirus Infections ,Sequence Analysis ,Sequence analysis ,hedgehog ,030106 microbiology ,Coronaviru ,Genome, Viral ,DNA sequencing ,Article ,Evolution, Molecular ,Betacoronavirus ,03 medical and health sciences ,symbols.namesake ,Eulipotyphla ,Phylogenetics ,Virology ,medicine ,Animals ,Pandemics ,Betacoronaviru ,Pandemic ,Animal ,Coronavirus Infection ,SARS-CoV-2 ,hedgehogs ,COVID-19 ,betacoronaviruses ,biology.organism_classification ,030104 developmental biology ,Sequence Analysi ,Sequence Alignment ,Middle East Respiratory Syndrome Coronaviru ,CD200 ortholog - Abstract
Due to their need for living cells, viruses have developed adaptive evolutionary strategies to survive and perpetuate in reservoir hosts that play a crucial role in the ecology of emerging pathogens. Pathogenic and potentially pandemic betacoronaviruses arose in humans in 2002 (SARS-CoV, disappeared in July 2003), 2012 (MERS-CoV, still circulating in Middle East areas), and 2019 (SARS-CoV-2, causing the current global pandemic). As universally recognized, bats host ancestors of the above-mentioned zoonotic viruses. However, hedgehogs have been recently identified in Europe and Asia as possible reservoirs of MERS-CoV-like strains classified as Erinaceus coronavirus (EriCoV). To elucidate the evolution and genetics of EriCoVs, NGS (next generation sequencing) and Sanger sequencing were used to examine fecal samples collected in Northern Italy in 2018/2019 from 12 hedgehogs previously found EriCoV-positive by RT-PCR. By sequence analysis, eight complete EriCoV genomes, obtained by NGS, showed a high phylogenetic correlation with EriCoV strains previously reported in Eurasia. Interestingly, eight viral strains presented an additional ORF encoding for the CD200 ortholog located between the genes encoding for the Spike and the ORF3a proteins. The CD200 ortholog sequences were closely similar to the host CD200 protein but varying among EriCoVs. The result, confirmed by Sanger sequencing, demonstrates for the first time that CoVs can acquire host genes potentially involved in the immune-modulatory cascade and possibly enabling the virus to escape the host defence.
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- 2020
47. Molecular Characterization of HEV Genotype 3 in Italy at Human/Animal Interface
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Anna Rosa Garbuglia, Luca De Sabato, Ilaria Di Bartolo, Maria Rosaria Capobianchi, and Daniele Lapa
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Microbiology (medical) ,Human animal ,viruses ,prevalence ,lcsh:QR1-502 ,Zoology ,hepatitis E virus ,medicine.disease_cause ,Microbiology ,lcsh:Microbiology ,subtype ,03 medical and health sciences ,Wild boar ,Hepatitis E virus ,biology.animal ,Genotype ,medicine ,030304 developmental biology ,Original Research ,0303 health sciences ,Phylogenetic tree ,biology ,030306 microbiology ,Transmission (medicine) ,Zoonosis ,virus diseases ,zoonosis ,Hepatitis E ,medicine.disease ,digestive system diseases ,Italy ,hepatitis E - Abstract
Hepatitis E virus (HEV) is an emerging public health issue in industrialized countries. In the last decade the number of autochthonous human infections has increased in Europe. Genotype 3 (HEV-3) is typically zoonotic, being foodborne the main route of transmission to humans, and is the most frequently detected in Europe in both humans and animals (mainly pigs and wild boars). In Italy, the first autochthonous human case was reported in 1999; since then, HEV-3 has been widely detected in both humans and animals. Despite the zoonotic characteristic of HEV-3 is well established, the correlation between animal and human strains has been poorly investigated in Italy. In the present study, we compared the subtype distribution of HEV-3 in humans and animals (swine and wild boar) in the period 2000–2018 from Italy. The dataset for this analysis included a total of 96 Italian ORF2 sequences (300 nt long), including both NCBI database-derived (n = 64) and recent sequences (2016–2018, n = 32) obtained in this study. The results show that subtype 3f is the most frequent in humans and pigs, followed by the HEV-3e, HEV-3c and other unassignable HEV-3 strains. Diversely, in wild boar a wider group of HEV-3 subtypes have been detected, including HEV-3a, which has also been detected for the first time in a human patient in Central Italy in 2017, and a wide group of unassignable HEV-3 strains. The phylogenetic analysis including, besides Italian strains, also sequences from other countries retrieved from the NCBI database, indicated that human Italian sequences, in particular those of HEV-3f and HEV-3e, form significant clusters mainly with sequences of animal origin from the same country. Nevertheless, for HEV-3c, rarely detected in Italian pigs, human sequences from Italy are more correlated to human sequences from other European countries. Furthermore, clusters of near-identical human strains identified in a short time interval in Lazio Region (Central Italy) can be recognized in the phylogenetic tree, suggesting that multiple infections originating from a common source have occurred, and confirming the importance of sequencing support to HEV surveillance.
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- 2019
48. Detection of Hepatitis E Virus in Livers and Muscle Tissues of Wild Boars in Italy
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Giovanni Ianiro, Antonino Barone, Luigi De Grossi, Claudia Esposito, Luca De Sabato, Giovanna Fusco, Maria Grazia Amoroso, Fabio Ostanello, Ilaria Di Bartolo, Enrica Martini, De Sabato L., Amoroso M.G., Ianiro G., Esposito C., De Grossi L., Fusco G., Barone A., Martini E., Ostanello F., and Di Bartolo I.
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0301 basic medicine ,Epidemiology ,Swine ,Health, Toxicology and Mutagenesis ,viruses ,030106 microbiology ,Population ,Sus scrofa ,Zoology ,Subtype ,010501 environmental sciences ,medicine.disease_cause ,Wild boar ,01 natural sciences ,03 medical and health sciences ,Hepatitis E virus ,Virology ,biology.animal ,Genotype ,medicine ,Animals ,education ,Gene ,Phylogeny ,0105 earth and related environmental sciences ,Swine Diseases ,education.field_of_study ,biology ,Phylogenetic tree ,Muscles ,Zoonosis ,virus diseases ,medicine.disease ,Hepatitis E ,Italy ,Liver ,HEV ,Muscle ,Food Science - Abstract
In industrialized countries, hepatitis E is now recognized as an emerging zoonosis. Autochthonous cases have been increased over recent years in Europe and are mainly associated with HEV-3 infections. Pigs and wild boars are considered the main reservoirs of the zoonotic HEV-3 and HEV-4 genotypes. Over the past decade, the number of wild boars has drastically increased in Europe. Due to habitats closer to humans and domestic animals, the role of wild boar as a reservoir of the zoonotic HEV is considered to be an emerging issue. In this study, we investigated the presence of HEV RNA by a real-time RT-PCR assay in paired liver and muscle samples collected from 196 wild boars (Sus scrofa) hunted in the two areas of Central and Southern Italy. Twenty animals (10.2%) were HEV RNA positive in livers, 11 of which were also positive in muscles. The ORF2 and ORF1 partial viral sequences were obtained for nine paired livers and muscles, and when aligned were identical to each other. Phylogenetic analyses confirmed detection of different HEV-3 subtypes: 3c, 3f, 3i and some that were not assigned to any subtypes that have so far been identified. Results need further investigation because they are based on analyses of sequences of short genome regions. Nevertheless, we observed that the same strains were circulating in the wild boar populations from the two investigated areas, confirming persistence of the same HEV strains in the wild boar population over time.
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- 2019
49. Occurrence of HEV-RNA in Italian Regional Pork and Wild Boar Food Products
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Palmiero Volzone, Luca De Sabato, Angela Michela Immacolata Montone, Federico Capuano, Benedetto Neola, Orlandina Di Maro, Elisabetta Suffredini, Alessandra Zaccherini, Ilaria Di Bartolo, and Mosè Alise
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0301 basic medicine ,Veterinary medicine ,Meat ,Virus Viability ,Genotype ,Epidemiology ,Swine ,Health, Toxicology and Mutagenesis ,030106 microbiology ,Sus scrofa ,010501 environmental sciences ,01 natural sciences ,03 medical and health sciences ,Wild boar ,Virology ,biology.animal ,medicine ,Hepatitis E virus ,Animals ,Humans ,Foodborne transmission ,Pork Liver ,Phylogeny ,0105 earth and related environmental sciences ,Swine Diseases ,biology ,virus diseases ,food and beverages ,Outbreak ,Hepatitis E ,medicine.disease ,Meat Products ,Italy ,Consumer Product Safety ,Food products ,Detection rate ,Food Science - Abstract
Hepatitis E is an emerging threat in industrialized countries. The foodborne transmission linked to consumption of pork and game meat is considered the main source of autochthonous infection. In Europe, small outbreaks have been reported linked to the consumption of pork liver sausages and wild boar meat. Based on previous findings and on increasing evidence of pork and game meat as a vehicle for HEV infections, the present study investigated the occurrence of HEV in 99 pork and 63 wild boar sausages and salami sold in Southern Italy. The HEV genome was detected in four wild boar sausages. Sequencing from 2 wild boar sausages confirmed that the HEV strains detected belonged to HEV-3 genotype, not assigned to any defined subtype. Data obtained confirmed the possible occurrence of HEV in pork products and in game. Although the detection rate is low, these products are frequently consumed raw after curing, whose effect on virus viability is still unknown.
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- 2019
50. Occurrence of two Norovirus outbreaks in the same cafeteria in one week
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Monini, M., Ostanello, F., Vignolo, E., Pagani, E., Gamper, S., Spertini, S., Masi, E., Rabini, M., Stenico, A., Poznanski, E., Ilaria Di Bartolo, Monini, Marina, Ostanello, Fabio, Vignolo, Edoardo, Pagani, Elisabetta, Gamper, Sabine, Spertini, Silvia, Masi, Elisa, Rabini, Michela, Stenico, Alberta, Poznanski, Elisa, and Di Bartolo, Ilaria
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Noroviru ,environmental contamination ,outbreak ,Food Handling ,Norovirus ,Food Contamination ,Disease Outbreaks ,Gastroenteritis ,Italy ,Environmental Microbiology ,Humans ,gastroenteriti ,foodborne ,Caliciviridae Infections - Abstract
In October 2017, two outbreaks of gastroenteritis (GE) occurred among patrons of a cafeteria in Italy in one week. Virological and bacteria investigations on stool samples, environment and food were conducted to identify the infectious agents and the possible source of infection. Forty-five cases occurred in the two outbreaks, including 13 laboratory-confirmed cases of norovirus GI. Nine staff members were interviewed, six were confirmed positive for NoV GI and 3 experienced GE symptoms. Bacteria faecal indicators and other bacteria pathogens were not detected in either environmental swab samples or food. A low level of NoV GII was detected in two environmental swab samples. The same GI.6 strain was identified in cases related to both outbreaks, suggesting a common source of infection. Since the two outbreaks occurred in one week, the NoV contamination could have persisted in the cafeteria. Furthermore, virological investigation revealed confirmed cases among food handlers who had worked at the cafeteria between and during the two outbreaks. Several studies highlighted the importance of excluding symptomatic food handlers to prevent contamination of foods and environment.
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- 2019
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