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Lavezzari D, Mori A, Pomari E, Deiana M, Fadda A, Bertoli L, Sinigaglia A, Riccetti S, Barzon L, Piubelli C, Delledonne M, Capobianchi MR, Castilletti C. Comparative analysis of bioinformatics tools to characterize SARS-CoV-2 subgenomic RNAs. Life Sci Alliance 2023; 6:e202302017. [PMID: 37748810 PMCID: PMC10520259 DOI: 10.26508/lsa.202302017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
During the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), positive-sense genomic RNA and subgenomic RNAs (sgRNAs) are synthesized by a discontinuous process of transcription characterized by a template switch, regulated by transcription-regulating sequences (TRS). Although poorly known about makeup and dynamics of sgRNAs population and function of its constituents, next-generation sequencing approaches with the help of bioinformatics tools have made a significant contribution to expand the knowledge of sgRNAs in SARS-CoV-2. For this scope to date, Periscope, LeTRS, sgDI-tector, and CORONATATOR have been developed. However, limited number of studies are available to compare the performance of such tools. To this purpose, we compared Periscope, LeTRS, and sgDI-tector in the identification of canonical (c-) and noncanonical (nc-) sgRNA species in the data obtained with the Illumina ARTIC sequencing protocol applied to SARS-CoV-2-infected Caco-2 cells, sampled at different time points. The three software showed a high concordance rate in the identification and in the quantification of c-sgRNA, whereas more differences were observed in nc-sgRNA. Overall, LeTRS and sgDI-tector result to be adequate alternatives to Periscope to analyze Fastq data from sequencing platforms other than Nanopore.
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Affiliation(s)
- Denise Lavezzari
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Antonio Mori
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Elena Pomari
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Michela Deiana
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Antonio Fadda
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Luca Bertoli
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Silvia Riccetti
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Chiara Piubelli
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | | | - Maria Rosaria Capobianchi
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Concetta Castilletti
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
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Cellular Landscaping of COVID-19 and Gynaecological Cancers: An Infrequent Correlation. JOURNAL OF ONCOLOGY 2022; 2022:5231022. [PMID: 36299504 PMCID: PMC9592241 DOI: 10.1155/2022/5231022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/16/2022] [Indexed: 01/08/2023]
Abstract
COVID-19 resulted in a mortality rate of 3–6% caused by SARS-CoV-2 and its variant leading to unprecedented consequences of acute respiratory distress septic shock and multiorgan failure. In such a situation, evaluation, diagnosis, treatment, and care for cancer patients are difficult tasks faced by medical staff. Moreover, patients with gynaecological cancer appear to be more prone to severe infection and mortality from COVID-19 due to immunosuppression by chemotherapy and coexisting medical disorders. To deal with such a circumtances oncologists have been obliged to reconsider the entire diagnostic, treatment, and management approach. This review will provide and discuss the molecular link with gynaecological cancer under COVID-19 infection, providing a novel bilateral relationship between the two infections. Moreover, the authors have provided insights to discuss the pathobiology of COVID-19 in gynaecological cancer and their risks associated with such comorbidity. Furthermore, we have depicted the overall impact of host immunity along with guidelines for the treatment of patients with gynaecological cancer under COVID-19 infection. We have also discussed the feasible scope for the management of COVID-19 and gynaecological cancer.
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Marcolungo L, Passera A, Maestri S, Segala E, Alfano M, Gaffuri F, Marturano G, Casati P, Bianco PA, Delledonne M. Real-Time On-Site Diagnosis of Quarantine Pathogens in Plant Tissues by Nanopore-Based Sequencing. Pathogens 2022; 11:pathogens11020199. [PMID: 35215142 PMCID: PMC8876587 DOI: 10.3390/pathogens11020199] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/23/2022] [Accepted: 01/29/2022] [Indexed: 12/31/2022] Open
Abstract
Rapid and sensitive assays for the identification of plant pathogens are necessary for the effective management of crop diseases. The main limitation of current diagnostic testing is the inability to combine broad and sensitive pathogen detection with the identification of key strains, pathovars, and subspecies. Such discrimination is necessary for quarantine pathogens, whose management is strictly dependent on genotype identification. To address these needs, we have established and evaluated a novel all-in-one diagnostic assay based on nanopore sequencing for the detection and simultaneous characterization of quarantine pathogens, using Xylella fastidiosa as a case study. The assay proved to be at least as sensitive as standard diagnostic tests and the quantitative results agreed closely with qPCR-based analysis. The same sequencing results also allowed discrimination between subspecies when present either individually or in combination. Pathogen detection and typing were achieved within 13 min of sequencing owing to the use of an internal control that allowed to stop sequencing when sufficient data had accumulated. These advantages, combined with the use of portable equipment, will facilitate the development of next-generation diagnostic assays for the efficient monitoring of other plant pathogens.
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Affiliation(s)
- Luca Marcolungo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (L.M.); (S.M.); (E.S.); (M.A.); (G.M.)
| | - Alessandro Passera
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milano, Via Celoria 2, 20133 Milan, Italy; (A.P.); (P.C.); (P.A.B.)
| | - Simone Maestri
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (L.M.); (S.M.); (E.S.); (M.A.); (G.M.)
| | - Elena Segala
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (L.M.); (S.M.); (E.S.); (M.A.); (G.M.)
| | - Massimiliano Alfano
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (L.M.); (S.M.); (E.S.); (M.A.); (G.M.)
| | - Francesca Gaffuri
- Servizio Fitosanitario Regione Lombardia Laboratorio Fitopatologico c/o Fondazione Minoprio, 22100 Minoprio, Italy;
| | - Giovanni Marturano
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (L.M.); (S.M.); (E.S.); (M.A.); (G.M.)
| | - Paola Casati
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milano, Via Celoria 2, 20133 Milan, Italy; (A.P.); (P.C.); (P.A.B.)
| | - Piero Attilio Bianco
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milano, Via Celoria 2, 20133 Milan, Italy; (A.P.); (P.C.); (P.A.B.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce, 73, 10135 Turin, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (L.M.); (S.M.); (E.S.); (M.A.); (G.M.)
- Genartis S.r.l., Via P. Mascagni 98, 37060 Castel D’Azzano, Italy
- Correspondence: ; Tel.: +39-045-802-7962
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Maestri S, Grosso V, Alfano M, Lavezzari D, Piubelli C, Bisoffi Z, Rossato M, Delledonne M. STArS (STrain-Amplicon-Seq), a targeted nanopore sequencing workflow for SARS-CoV-2 diagnostics and genotyping. Biol Methods Protoc 2022; 7:bpac020. [PMID: 36046362 PMCID: PMC9422081 DOI: 10.1093/biomethods/bpac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Diagnostic tests based on reverse transcription–quantitative polymerase chain reaction (RT–qPCR) are the gold standard approach to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from clinical specimens. However, unless specifically optimized, this method is usually unable to recognize the specific viral strain responsible of coronavirus disease 2019, a crucial information that is proving increasingly important in relation to virus spread and treatment effectiveness. Even if some RT–qPCR commercial assays are currently being developed for the detection of viral strains, they focus only on single/few genetic variants that may not be sufficient to uniquely identify a specific strain. Therefore, genome sequencing approaches remain the most comprehensive solution for virus genotyping and to recognize viral strains, but their application is much less widespread due to higher costs. Starting from the well-established ARTIC protocol coupled to nanopore sequencing, in this work, we developed STArS (STrain-Amplicon-Seq), a cost/time-effective sequencing-based workflow for both SARS-CoV-2 diagnostics and genotyping. A set of 10 amplicons was initially selected from the ARTIC tiling panel, to cover: (i) all the main biologically relevant genetic variants located on the Spike gene; (ii) a minimal set of variants to uniquely identify the currently circulating strains; (iii) genomic sites usually amplified by RT–qPCR method to identify SARS-CoV-2 presence. PCR-amplified clinical samples (both positive and negative for SARS-CoV-2 presence) were pooled together with a serially diluted exogenous amplicon at known concentration and sequenced on a MinION device. Thanks to a scoring rule, STArS had the capability to accurately classify positive samples in agreement with RT–qPCR results, both at the qualitative and quantitative level. Moreover, the method allowed to effectively genotype strain-specific variants and thus also return the phylogenetic classification of SARS-CoV-2-postive samples. Thanks to the reduced turnaround time and costs, the proposed approach represents a step towards simplifying the clinical application of sequencing for viral genotyping, hopefully aiding in combatting the global pandemic.
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Affiliation(s)
- Simone Maestri
- Department of Biotechnology, University of Verona , 37134 Verona, Italy
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia , 20139 Milano, Italy
| | - Valentina Grosso
- Department of Biotechnology, University of Verona , 37134 Verona, Italy
| | | | - Denise Lavezzari
- Department of Biotechnology, University of Verona , 37134 Verona, Italy
| | - Chiara Piubelli
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital , 37024 Verona, Italy
| | - Zeno Bisoffi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital , 37024 Verona, Italy
- Department of Diagnostics and Public Health, University of Verona , 37134, Verona, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona , 37134 Verona, Italy
- Genartis srl , 37126 Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona , 37134 Verona, Italy
- Genartis srl , 37126 Verona, Italy
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Grandi N, Paglietti B, Cusano R, Ibba G, Lai V, Piu C, Angioj F, Serra C, Kelvin DJ, Tramontano E, Rubino S. Genomic Snapshot of SARS-CoV-2 in Migrants Entering Through Mediterranean Sea Routes. Front Public Health 2022; 10:846115. [PMID: 35309205 PMCID: PMC8927662 DOI: 10.3389/fpubh.2022.846115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/07/2022] [Indexed: 02/05/2023] Open
Abstract
In December 2019, a novel coronavirus emerged in Wuhan, China, rapidly spreading into a global pandemic. Italy was the first European country to experience SARS-CoV-2 epidemic, and one of the most severely affected during the first wave of diffusion. In contrast to the general restriction of people movements in Europe, the number of migrants arriving at Italian borders via the Mediterranean Sea route in the summer of 2020 had increased dramatically, representing a possible, uncontrolled source for the introduction of novel SARS-CoV-2 variants. Importantly, most of the migrants came from African countries showing limited SARS-CoV-2 epidemiological surveillance. In this study, we characterized the SARS-CoV-2 genome isolated from an asymptomatic migrant arrived in Sardinia via the Mediterranean route in September 2020, in comparison with SARS-CoV-2 isolates arrived in Sicily through the Libyan migration route; with SARS-CoV-2 isolates circulating in Sardinia during 2020; and with viral genomes reported in African countries during the same summer. Results showed that our sequence is not phylogenetically related to isolates from migrants arriving in Sicily, nor to isolates circulating in Sardinia territory, having greater similarity to SARS-CoV-2 genomes reported in countries known for being sites of migrant embarkation to Italy. This is in line with the hypothesis that most SARS-CoV-2 infections among migrants have been acquired prior to embarking to Italy, possibly during the travel to or the stay in crowded Libyan immigrant camps. Overall, these observations underline the importance of dedicated SARS-CoV-2 surveillance of migrants arriving in Italy and in Europe through the Mediterranean routes.
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Affiliation(s)
- Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Bianca Paglietti
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
- *Correspondence: Bianca Paglietti
| | - Roberto Cusano
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), Science and Technology Park Polaris, Cagliari, Italy
| | - Gabriele Ibba
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - Vincenzo Lai
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - Claudia Piu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - Flavia Angioj
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - Caterina Serra
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - David J. Kelvin
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, China
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale Delle Ricerche, Cagliari, Italy
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC Microbiologia e Virologia, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
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Caldrer S, Mazzi C, Bernardi M, Prato M, Ronzoni N, Rodari P, Angheben A, Piubelli C, Tiberti N. Regulatory T Cells as Predictors of Clinical Course in Hospitalised COVID-19 Patients. Front Immunol 2021; 12:789735. [PMID: 34925369 PMCID: PMC8674838 DOI: 10.3389/fimmu.2021.789735] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/15/2021] [Indexed: 12/25/2022] Open
Abstract
Background The host immune response has a prominent role in the progression and outcome of SARS-CoV-2 infection. Lymphopenia has been described as an important feature of SARS-CoV-2 infection and has been associated with severe disease manifestation. Lymphocyte dysregulation and hyper-inflammation have been shown to be associated with a more severe clinical course; however, a T cell subpopulation whose dysfunction correlate with disease progression has yet to be identify. Methods We performed an immuno-phenotypic analysis of T cell sub-populations in peripheral blood from patients affected by different severity of COVID-19 (n=60) and undergoing a different clinical evolution. Clinical severity was established based on a modified WHO score considering both ventilation support and respiratory capacity (PaO2/FiO2 ratio). The ability of circulating cells at baseline to predict the probability of clinical aggravation was explored through multivariate regression analyses. Results The immuno-phenotypic analysis performed by multi-colour flow cytometry confirmed that patients suffering from severe COVID-19 harboured significantly reduced circulating T cell subsets, especially for CD4+ T, Th1, and regulatory T cells. Peripheral T cells also correlated with parameters associated with disease severity, i.e., PaO2/FiO2 ratio and inflammation markers. CD4+ T cell subsets showed an important significant association with clinical evolution, with patients presenting markedly decreased regulatory T cells at baseline having a significantly higher risk of aggravation. Importantly, the combination of gender and regulatory T cells allowed distinguishing between improved and worsened patients with an area under the ROC curve (AUC) of 82%. Conclusions The present study demonstrates the association between CD4+ T cell dysregulation and COVID-19 severity and progression. Our results support the importance of analysing baseline regulatory T cell levels, since they were revealed able to predict the clinical worsening during hospitalization. Regulatory T cells assessment soon after hospital admission could thus allow a better clinical stratification and patient management.
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Affiliation(s)
- Sara Caldrer
- Department of Infectious - Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Sacro Cuore - Don Calabria Hospital, Verona, Italy
| | - Cristina Mazzi
- Centre for Clinical Research, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Sacro Cuore - Don Calabria Hospital, Verona, Italy
| | - Milena Bernardi
- Department of Infectious - Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Sacro Cuore - Don Calabria Hospital, Verona, Italy
| | - Marco Prato
- Department of Infectious - Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Sacro Cuore - Don Calabria Hospital, Verona, Italy
| | - Niccolò Ronzoni
- Department of Infectious - Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Sacro Cuore - Don Calabria Hospital, Verona, Italy
| | - Paola Rodari
- Department of Infectious - Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Sacro Cuore - Don Calabria Hospital, Verona, Italy
| | - Andrea Angheben
- Department of Infectious - Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Sacro Cuore - Don Calabria Hospital, Verona, Italy
| | - Chiara Piubelli
- Department of Infectious - Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Sacro Cuore - Don Calabria Hospital, Verona, Italy
| | - Natalia Tiberti
- Department of Infectious - Tropical Diseases and Microbiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Sacro Cuore - Don Calabria Hospital, Verona, Italy
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