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1دورية أكاديمية
المؤلفون: Michela Deiana, Denise Lavezzari, Antonio Mori, Silvia Accordini, Elena Pomari, Chiara Piubelli, Simone Malagò, Maddalena Cordioli, Niccolò Ronzoni, Andrea Angheben, Evelina Tacconelli, Maria Rosaria Capobianchi, Federico Giovanni Gobbi, Concetta Castilletti
المصدر: Viruses, Vol 16, Iss 5, p 726 (2024)
مصطلحات موضوعية: monkeypox virus (MPXV), mpox outbreak, next-generation sequencing (NGS), mutations, APOBEC3 intra-patient variation, single nucleotide variant (SNV), Microbiology, QR1-502
الوصف: In 2022, an unprecedented outbreak of mpox raged in several nations. Sequences from the 2022 outbreak reveal a higher nucleotide substitution if compared with the estimated rate for orthopoxviruses. Recently, intra-lesion SNVs (single nucleotide variants) have been described, and these have been suggested as possible sources of genetic variation. Until now, it has not been clear if the presence of several SNVs could represents the result of local mutagenesis or a possible co-infection. We investigated the significance of SNVs through whole-genome sequencing analysis of four unrelated mpox cases. In addition to the known mutations harboured by the circulating strains of virus (MPXV), 7 novel mutations were identified, including SNVs located in genes that are involved in immune evasion mechanisms and/or viral fitness, six of these appeared to be APOBEC3-driven. Interestingly, three patients exhibited the coexistence of mutated and wild-type alleles for five non-synonymous variants. In addition, two patients, apparently unrelated, showed an analogous pattern for two novel mutations, albeit with divergent frequencies. The coexistence of mixed viral populations, harbouring non-synonymous mutations in patients, supports the hypothesis of possible co-infection. Additional investigations of larger clinical cohorts are essential to validating intra-patient viral genome heterogeneity and determining the possibility of co-presence events of slightly divergent MPXV strains.
وصف الملف: electronic resource
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2دورية أكاديمية
المؤلفون: Chiara Piubelli, Davide Treggiari, Denise Lavezzari, Michela Deiana, Klevia Dishnica, Emma Maria Sole Tosato, Cristina Mazzi, Paolo Cattaneo, Antonio Mori, Elena Pomari, Lavinia Nicolini, Martina Leonardi, Francesca Perandin, Fabio Formenti, Alejandro Giorgetti, Antonio Conti, Maria Rosaria Capobianchi, Federico Giovanni Gobbi, Concetta Castilletti
المصدر: Viruses, Vol 16, Iss 5, p 657 (2024)
مصطلحات موضوعية: SARS-CoV-2, diagnosis, antigenic rapid test, molecular test, nucleocapsid protein, Omicron variant, Microbiology, QR1-502
الوصف: With the continuous spread of new SARS-CoV-2 variants of concern (VOCs), the monitoring of diagnostic test performances is mandatory. We evaluated the changes in antigen diagnostic tests’ (ADTs) accuracy along the Delta to Omicron VOCs transition, exploring the N protein mutations possibly affecting ADT sensitivity and assessing the best sampling site for the diagnosis of Omicron infections. In total, 5175 subjects were enrolled from 1 October 2021 to 15 July 2022. The inclusion criteria were SARS-CoV-2 ADT combined with a same-day RT-PCR swab test. For the sampling site analysis, 61 patients were prospectively recruited during the Omicron period for nasal and oral swab analyses by RT-PCR. Next-Generation Sequencing data were obtained to evaluate the different sublineages. Using RT-PCR as a reference, 387 subjects resulted in becoming infected and the overall sensitivity of the ADT decreased from 63% in the Delta period to 33% in the Omicron period. This decrease was highly statistically significant (p < 0.001), and no decrease in viral load was detected at the RNA level. The nasal site presented a significantly higher viral load than the oral site during the Omicron wave. The reduced detection rate of Omicron infections by ADT should be considered in the global testing strategy to preserve accurate diagnoses across the changing SARS-CoV-2 variants.
وصف الملف: electronic resource
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3دورية أكاديمية
المؤلفون: Antonio Mori, Andrea Matucci, Elena Pomari, Silvia Accordini, Chiara Piubelli, Annalisa Donini, Lavinia Nicolini, Concetta Castilletti
المصدر: Viruses, Vol 16, Iss 1, p 98 (2024)
مصطلحات موضوعية: Toscana virus, urine, real-time RT-PCR, analytical proof-of-concept study, Microbiology, QR1-502
الوصف: Toscana virus (TOSV), a sandfly-borne virus, is an important etiological agent in human acute meningitis and meningoencephalitis in the Mediterranean area during the summer. However, the actual number of TOSV infections is underestimated. Laboratory confirmation is necessary because TOSV infection has overlapping clinical features with other neuro-invasive viral infections. Nowadays, the reference test for direct diagnosis in the acute phase of TOSV infection is the PCR based method for detecting TOSV in cerebrospinal fluid and/or plasma, serum, or blood. Although poorly employed, urine is another helpful biological matrix for TOSV detection. Urine is a matrix rich in PCR inhibitors that affect PCR efficiency; consequently, false negatives could be generated. To investigate the potential effect of urine PCR inhibitors on TOSV detection, we compared undiluted and diluted urine using 10-fold series of spiked TOSV. The results showed a significant improvement in TOSV detection performance in diluted urine (1 TCID50 vs. 1 × 104 TCID50 limit of detection and 101.35% vs. 129.62% efficiency, respectively, in diluted and undiluted urine). In conclusion, our data provide preliminary important insights into the use of diluted urine to limit the impact of the inhibitory effects of urine on the detection of TOSV in RT-PCR-based approaches.
وصف الملف: electronic resource
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4دورية أكاديمية
المؤلفون: Elena Pomari, Giovanni Malerba, Laura Veschetti, Alessandra Franceschi, Lucas Moron Dalla Tor, Michela Deiana, Monica Degani, Manuela Mistretta, Cristina Patuzzo, Andrea Ragusa, Antonio Mori, Zeno Bisoffi, Dora Buonfrate
المصدر: Scientific Reports, Vol 12, Iss 1, Pp 1-12 (2022)
الوصف: Abstract Strongyloidiasis is a neglected tropical disease caused by the soil-transmitted nematode by Strongyloides stercoralis, that affects approximately 600 million people worldwide. In immunosuppressed individuals disseminated strongyloidiasis can rapidly lead to fatal outcomes. There is no gold standard for diagnosing strongyloidiasis, and infections are frequently misdiagnosed. A better understanding of the molecular biology of this parasite can be useful for example for the discovery of potential new biomarkers. Interestingly, recent evidence showed the presence of small RNAs in Strongyloididae, but no data was provided for S. stercoralis. In this study, we present the first identification of miRNAs of both L1 and iL3 larval stages of S. stercoralis. For our purpose, the aims were: (i) to analyse the miRNome of L1 and iL3 S. stercoralis and to identify potential miRNAs of this nematode, (ii) to obtain the mRNAs profiles in these two larval stages and (iii) to predict potential miRNA target sites in mRNA sequences. Total RNA was isolated from L1 and iL3 collected from the stool of 5 infected individuals. For the miRNAs analysis, we used miRDeep2 software and a pipeline of bio-informatic tools to construct a catalog of a total of 385 sequences. Among these, 53% were common to S. ratti, 19% to S. papillosus, 1% to Caenorhabditis elegans and 44% were novel. Using a differential analysis between the larval stages, we observed 6 suggestive modulated miRNAs (STR-MIR-34A-3P, STR-MIR-8397-3P, STR-MIR-34B-3P and STR-MIR-34C-3P expressed more in iL3, and STR-MIR-7880H-5P and STR-MIR-7880M-5P expressed more in L1). Along with this analysis, we obtained also the mRNAs profiles in the same samples of larvae. Multiple testing found 81 statistically significant mRNAs of the total 1553 obtained (FDR
وصف الملف: electronic resource
العلاقة: https://doaj.org/toc/2045-2322Test
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5دورية أكاديمية
المؤلفون: Antonio Mori, Denise Lavezzari, Elena Pomari, Michela Deiana, Chiara Piubelli, Maria Rosaria Capobianchi, Concetta Castilletti
المصدر: Aspects of Molecular Medicine, Vol 1, Iss , Pp 100008- (2023)
مصطلحات موضوعية: sgRNAs, SARS-CoV2, Bioinformatics, Next-generation sequencing, Viruses, Coronavirus, Medicine
الوصف: Like for other coronaviruses, SARS-CoV-2 gene expression strategy is based on the synthesis of a nested set of subgenomic mRNA species (sgRNAs). These sgRNA are synthesized using a “discontinuous transcription” mechanism that relies on template switching at Transcription Regulatory Sequences (TRS). Both canonical (c-sgRNA) and non-canonical (nc-sgRNA, less numerous) subgenomic RNA species can be produced. Currently, sgRNAs are investigated on the basis of sequence data obtained through next generation sequencing (NGS), and bioinformatic tools are crucial for their identification, characterization and quantification. To date, few software have been developed to this aim, whose reliability and applicability to all the available NGS platforms need to be established, to build confidence on the information resulting from such tools. In fact, these information may be crucial for the in depth elucidation of viral expression strategy, particularly in respect of the significance of nc-sgRNAs, and for the possible use of sgRNAs as potential markers of virus replicative activity in infected patients.
وصف الملف: electronic resource
العلاقة: http://www.sciencedirect.com/science/article/pii/S2949688823000084Test; https://doaj.org/toc/2949-6888Test
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6دورية أكاديمية
المؤلفون: Maria Rosaria Capobianchi, Antonino Di Caro, Chiara Piubelli, Antonio Mori, Zeno Bisoffi, Concetta Castilletti
المصدر: Frontiers in Cellular and Infection Microbiology, Vol 12 (2022)
مصطلحات موضوعية: monkeypox, prevention measures, seroepidemiology, subclinical infection, animal reservoir, spillover, Microbiology, QR1-502
الوصف: Starting from mid-May 2022, cases of human monkeypox started to rise in several non-endemic countries. By mid-July, more than 17000 confirmed/suspect cases have been reported by at least 82 countries worldwide, with a regular incremental trend. In order to contain the disease diffusion, risk evaluation is crucial to undertake informed decisions and effective communication campaigns. However, since orthopoxvirus infections so far have attracted low attention, due to the eradication of smallpox 40 years ago, and to the confinement of human monkeypox almost exclusively to endemic areas, several unresolved issues concerning natural history, ecology and pathogenesis remain. To this respect, we identified some open questions and reviewed the relevant literature on monkeypoxvirus and/or related orthopoxviruses. The results will be discussed in the perspective of their relevance to public health decisions, particularly those related to non-pharmacological interventions.
وصف الملف: electronic resource
العلاقة: https://www.frontiersin.org/articles/10.3389/fcimb.2022.1005955/fullTest; https://doaj.org/toc/2235-2988Test
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7دورية أكاديمية
المؤلفون: Giulio Innamorati, Thomas M. Wilkie, Giorgio Malpeli, Salvatore Paiella, Silvia Grasso, Borislav Rusev, Biagio Eugenio Leone, Maria Teresa Valenti, Luca dalle Carbonare, Samuele Cheri, Alice Giacomazzi, Marco Zanotto, Vanessa Guardini, Michela Deiana, Donato Zipeto, Michela Serena, Marco Parenti, Francesca Guzzi, Rita Teresa Lawlor, Giovanni Malerba, Antonio Mori, Giuseppe Malleo, Luca Giacomello, Roberto Salvia, Claudio Bassi
المصدر: Scientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
الوصف: Abstract The GNA15 gene is ectopically expressed in human pancreatic ductal adenocarcinoma cancer cells. The encoded Gα15 protein can promiscuously redirect GPCR signaling toward pathways with oncogenic potential. We sought to describe the distribution of GNA15 in adenocarcinoma from human pancreatic specimens and to analyze the mechanism driving abnormal expression and the consequences on signaling and clinical follow-up. We detected GNA15 expression in pre-neoplastic pancreatic lesions and throughout progression. The analysis of biological data sets, primary and xenografted human tumor samples, and clinical follow-up shows that elevated expression is associated with poor prognosis for G NA 15, but not any other GNA gene. Demethylation of the 5′ GNA15 promoter region was associated with ectopic expression of Gα15 in pancreatic neoplastic cells, but not in adjacent dysplastic or non-transformed tissue. Down-modulation of Gα15 by shRNA or CRISPR/Cas9 affected oncogenic signaling, and reduced adenocarcimoma cell motility and invasiveness. We conclude that de novo expression of wild-type GNA15 characterizes transformed pancreatic cells. The methylation pattern of GNA15 changes in preneoplastic lesions coincident with the release a transcriptional blockade that allows ectopic expression to persist throughout PDAC progression. Elevated GNA15 mRNA correlates with poor prognosis. In addition, ectopic Gα15 signaling provides an unprecedented mechanism in the early steps of pancreas carcinogenesis distinct from classical G protein oncogenic mutations described previously in GNAS and GNAQ/GNA11.
وصف الملف: electronic resource
العلاقة: https://doaj.org/toc/2045-2322Test
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8دورية أكاديمية
المؤلفون: Elena Pomari, Antonio Mori, Silvia Accordini, Annalisa Donini, Maddalena Cordioli, Evelina Tacconelli, Concetta Castilletti
المصدر: Diagnostics, Vol 13, Iss 7, p 1349 (2023)
مصطلحات موضوعية: ddPCR, quantification, DNA, monkeypox virus, Medicine (General), R5-920
الوصف: Background: Monkeypox virus (MPXV) is a double-stranded DNA virus belonging to the orthopoxvirus genus in the family Poxviridae. Distinct clades are identified: the clade I belonging to the Central African (or Congo Basin) clade and the subclades IIa and IIb belonging to the West African clade. Here, a commercial droplet digital PCR (ddPCR) assay was evaluated for the quantification of the MPXV West Africa clade in clinical samples. Methods: The ddPCR reaction was assessed as a duplex assay using RPP30 as an internal amplification control. A total of 60 clinical specimens were tested, 40 positives (skin lesions, n=10; rectal swabs, n = 10; pharyngeal swabs, n = 10; and whole blood, n = 10), and 20 negatives (n = 5 for each biological matrix) were found at the routine molecular diagnostics (orthopoxvirus qPCR followed by confirmation with Sanger sequencing). To evaluate the analytical sensitivity, the ddPCR reaction was first analyzed on serial dilutions of synthetic DNA spiked in water and in negative biological matrices, achieving a limit of detection of 3.5 copy/µL. Results: Regarding the clinical samples, compared to routine molecular diagnostics, the ddPCR duplex assay showed 100% of specificity for all biological matrices and 100% sensitivity (10/10) for lesions, 100% (10/10) for rectal swabs, 90% (9/10) for pharyngeal swabs, and 60% (6/10) for whole blood. Conclusion: Overall, our data showed that the commercial ddPCR assay allowed the DNA detection of MPXV in 87.5% (35/40) of our cohort, highlighting useful technical indications for the different specimens with a potential greatest performance for skin lesions and rectal swabs.
وصف الملف: electronic resource
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9دورية أكاديمية
المؤلفون: Anna Beltrame, Maria Concetta Fargnoli, Charlotte Avanzi, Laura Sollima, Elena Pomari, Antonio Mori, Silvia Stefania Longoni, Lucia Moro, Pierantonio Orza, Mary Jackson, Francesca Perandin
المصدر: Pathogens, Vol 12, Iss 2, p 165 (2023)
الوصف: Coupled with its rarity in non-endemic areas, the clinical heterogeneity of leprosy makes diagnosis very challenging. We report a diagnosis of multibacillary leprosy in a 22-year-old Indian woman, adopted at the age of 10 and living in Italy. The patient presented with painful skin lesions on the face, trunk, and lower and upper extremities, associated with dysesthesia and a motor deficit in her left leg following corticosteroid therapy interruption. Histopathology results from the skin lesions suggested leprosy, but no acid-fast bacilli were identified. Molecular biology in a center specializing in tropical diseases confirmed the diagnosis, allowing prompt and adequate treatment. Genotype analysis allowed the identification of a genotype 1D of M. leprae, facilitating the epidemiological investigation of the plausible infection origin. No resistances to rifampicin, dapsone, or ofloxacin were detected. Leprosy will continue to exist in high-income nations, and the incidence may rise over time due to increasing migration and globalization. CARE guidelines were followed.
وصف الملف: electronic resource
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10دورية أكاديمية
المؤلفون: Michela Deiana, Antonio Mori, Chiara Piubelli, Francesca Perandin, Davide Treggiari, Davide Martini, Fabio Chesini, Andrea Angheben, Francesco Bonfante, Calogero Terregino, Zeno Bisoffi, Elena Pomari
المصدر: Microorganisms, Vol 9, Iss 8, p 1738 (2021)
مصطلحات موضوعية: SARS-CoV-2, coronavirus, subgenomic, saliva, vaccine, BNT162b2, Biology (General), QH301-705.5
الوصف: SARS-CoV-2 infection was monitored in 1898 health care workers (HCWs) after receiving full vaccination with BNT162b2. Untill 30 June 2021, 10 HCWs tested positive for SARS-CoV-2 using real time RT-PCR, resulting in a 4-month cumulative incidence of 0.005%. The infection was mildly symptomatic in six (60%) and asymptomatic in four (40%) individuals. Among the infected HCWs, eight consenting individuals provided paired NPS and saliva during the course of infection, for the purpose of the analysis performed in the present study. Genomic and subgenomic viral RNAs were investigated using real-time RT-PCR in both biological specimens. The temporal profile of viral load was measured using ddPCR. Viral mutations were also analysed. Subgenomic viral RNA was detected in 8/8 (100%) NPS and in 6/8 (75%) saliva specimens at the baseline. The expression of subgenomic RNA was observed for up to 7 days in 3/8 (38%) symptomatic cases. Moreover, concordance was observed between NPS and saliva in the detection of viral mutations, and both N501Y and 69/70del (associated with the B.1.1.7 variant) were detected in the majority 6/8 (75%) of subjects, while the K417T mutation (associated with the P.1-type variants) was detected in 2/8 (25%) individuals. Overall, our findings report a low frequency of infected HCWs after full vaccination. It is, therefore, important to monitor the vaccinees in order to identify asymptomatic infected individuals. Saliva can be a surrogate for SARS-CoV-2 surveillance, particularly in social settings such as hospitals.
وصف الملف: electronic resource
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