16 results on '"Cesare Ernesto Maria Gruber"'
Search Results
2. Temporal intra‐host variability of mpox virus genomes in multiple body tissues
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Martina Rueca, Fabio Giovanni Tucci, Valentina Mazzotta, Giulia Gramigna, Cesare Ernesto Maria Gruber, Lavinia Fabeni, Emanuela Giombini, Giulia Matusali, Carmela Pinnetti, Andrea Mariano, Ornella Butera, Eliana Specchiarello, Annalisa Mondi, Simone Lanini, Fabrizio Carletti, Enrico Girardi, Francesco Vaia, Emanuele Nicastri, Andrea Antinori, and Fabrizio Maggi
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Infectious Diseases ,Virology - Published
- 2023
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3. Genomic surveillance of SARS-CoV-2 positive passengers on flights from China to Italy, December 2022
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Federica Novazzi, Emanuela Giombini, Martina Rueca, Andreina Baj, Lavinia Fabeni, Angelo Genoni, Francesca Drago Ferrante, Giulia Gramigna, Cesare Ernesto Maria Gruber, Sara Boutahar, Claudia Minosse, Ornella Butera, Renee Pasciuta, Daniele Focosi, Alberto Colombo, Andrea Antinori, Enrico Girardi, Francesco Vaia, and Fabrizio Maggi
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Epidemiology ,Virology ,Public Health, Environmental and Occupational Health - Abstract
With numbers of COVID-19 cases having substantially increased at the end of 2022 in China, some countries have started or expanded testing and genomic surveillance of travellers. We report screening results in Italy in late December 2022 of 556 flight passengers in provenance from two Chinese provinces. Among these passengers, 126 (22.7%) tested SARS-CoV-2 positive. Whole genome sequencing of 61 passengers’ positive samples revealed Omicron variants, notably sub-lineages BA.5.2.48, BF.7.14 and BQ.1.1, in line with data released from China.
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- 2023
4. Epidemiological, clinical and virological characteristics of four cases of monkeypox support transmission through sexual contact, Italy, May 2022
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Andrea, Antinori, Valentina, Mazzotta, Serena, Vita, Fabrizio, Carletti, Danilo, Tacconi, Laura Emma, Lapini, Alessandra, D'Abramo, Stefania, Cicalini, Daniele, Lapa, Silvia, Pittalis, Vincenzo, Puro, Marco, Rivano Capparuccia, Emanuela, Giombini, Cesare Ernesto Maria, Gruber, Anna Rosa, Garbuglia, Alessandra, Marani, Francesco, Vairo, Enrico, Girardi, Francesco, Vaia, Emanuele, Nicastri, and Alessandra, Vergori
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Male ,Young Adult ,Semen ,Epidemiology ,Sexual Behavior ,Virology ,Public Health, Environmental and Occupational Health ,Humans ,Monkeypox ,Monkeypox virus ,Disease Outbreaks - Abstract
Since May 2022, an outbreak of monkeypox has been ongoing in non-endemic countries. We report four cases in Italy in young adult men reporting condomless sexual intercourse. The patients are in good clinical condition with no need for specific antiviral drugs. Biological samples from seminal fluid were positive for monkeypox viral DNA. For many other viruses found in semen there is no evidence of sexual transmission. The possibility of sexual transmission of monkeypox virus needs to be investigated.
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- 2022
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5. SARS-CoV-2 Phylogenetic Analysis, Lazio Region, Italy, February–March 2020
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Emanuela Giombini, Cesare Ernesto Maria Gruber, Antonino Di Caro, Francesco Messina, Eleonora Lalle, Barbara Bartolini, Giuseppe Ippolito, Francesca Colavita, Martina Rueca, Concetta Castilletti, Giulia Matusali, Maria Rosaria Capobianchi, Fabrizio Carletti, Francesco Vairo, and Licia Bordi
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Male ,Time Factors ,Epidemiology ,viruses ,lcsh:Medicine ,Severity of Illness Index ,COVID-19 Testing ,0302 clinical medicine ,Nasopharynx ,Pandemic ,full genome sequence ,Prospective Studies ,030212 general & internal medicine ,Clade ,Phylogeny ,biology ,Phylogenetic tree ,Dispatch ,High-Throughput Nucleotide Sequencing ,Middle Aged ,Hospitalization ,Infectious Diseases ,Lazio region ,Italy ,coronavirus disease ,RNA, Viral ,Female ,Coronavirus Infections ,Bronchoalveolar Lavage Fluid ,severe acute respiratory syndrome coronavirus 2 ,Adult ,Microbiology (medical) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Pneumonia, Viral ,030231 tropical medicine ,Real-Time Polymerase Chain Reaction ,Virus ,lcsh:Infectious and parasitic diseases ,Betacoronavirus ,03 medical and health sciences ,respiratory infections ,Phylogenetics ,SARS-CoV-2 Phylogenetic Analysis, Lazio Region, Italy, February–March 2020 ,Humans ,lcsh:RC109-216 ,phylogenetic tree ,Pandemics ,Aged ,Clinical Laboratory Techniques ,SARS-CoV-2 ,lcsh:R ,COVID-19 ,biology.organism_classification ,Virology ,Mutation - Abstract
We report phylogenetic and mutational analysis of severe acute respiratory syndrome coronavirus 2 virus strains from the Lazio region of Italy and provide information about the dynamics of virus spread. Data suggest effective containment of clade V strains, but subsequently, multiple waves of clade G strains were circulating widely in Europe.
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- 2020
6. Laboratory management of Crimean-Congo haemorrhagic fever virus infections: perspectives from two European networks
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Chantal Reusken, Hervé Zeller, Gulay Korukluoglu, Anna Papa, Cinthia Menel Lemos, Roger Hewson, Barbara Bartolini, Ali Mirazimi, Giuseppe Ippolito, Cesare Ernesto Maria Gruber, Antonino Di Caro, Roland Grunow, María Paz Sánchez-Seco, Sylvia Bino, Marion Koopmans, Aisha V. Sauer, Tatjana Avšič, Carla Nisii, Iva Christova, Maria Rosaria Capobianchi, Virology, Unión Europea, European Centre for Disease Prevention and Control, and Unión Europea. Comisión Europea
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0301 basic medicine ,Laboratory Proficiency Testing ,Epidemiology ,Review ,Disease ,emerging diseases ,Communicable Diseases, Emerging ,Disease Outbreaks ,Biosafety ,Ticks ,Infection control ,media_common ,Emerging diseases ,Crimean-Congo haemorrhagic fever virus ,3. Good health ,Preparedness ,Hemorrhagic Fever Virus, Crimean-Congo ,Emerging infectious disease ,medicine.medical_specialty ,Ixodidae ,030106 microbiology ,Enzyme-Linked Immunosorbent Assay ,03 medical and health sciences ,Virology ,CCHF ,medicine ,Animals ,Humans ,laboratory preparedness ,media_common.cataloged_instance ,ddc:610 ,European union ,Intensive care medicine ,laboratory response ,Clinical Laboratory Techniques ,Sequence Analysis, RNA ,business.industry ,Public health ,Public Health, Environmental and Occupational Health ,Outbreak ,European network ,030104 developmental biology ,CCHFV ,Immunoglobulin G ,Laboratory preparedness ,DNA, Viral ,Hemorrhagic Fever, Crimean ,Laboratories ,610 Medizin und Gesundheit ,business ,Laboratory response - Abstract
Background Crimean-Congo haemorrhagic fever virus (CCHFV) is considered an emerging infectious disease threat in the European Union. Since 2000, the incidence and geographic range of confirmed CCHF cases have markedly increased, following changes in the distribution of its main vector, Hyalomma ticks. Aims To review scientific literature and collect experts’ opinion to analyse relevant aspects of the laboratory management of human CCHF cases and any exposed contacts, as well as identify areas for advancement of international collaborative preparedness and laboratory response plans. Methods We conducted a literature review on CCHF molecular diagnostics through an online search. Further, we obtained expert opinions on the key laboratory aspects of CCHF diagnosis. Consulted experts were members of two European projects, EMERGE (Efficient response to highly dangerous and emerging pathogens at EU level) and EVD-LabNet (Emerging Viral Diseases-Expert Laboratory Network). Results Consensus was reached on relevant and controversial aspects of CCHF disease with implications for laboratory management of human CCHF cases, including biosafety, diagnostic algorithm and advice to improve lab capabilities. Knowledge on the diffusion of CCHF can be obtained by promoting syndromic approach to infectious diseases diagnosis and by including CCHFV infection in the diagnostic algorithm of severe fevers of unknown origin. Conclusion No effective vaccine and/or therapeutics are available at present so outbreak response relies on rapid identification and appropriate infection control measures. Frontline hospitals and reference laboratories have a crucial role in the response to a CCHF outbreak, which should integrate laboratory, clinical and public health responses.
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- 2019
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7. Late Relapse and Reinfection in HCV Patients Treated with Direct-Acting Antiviral (DAA) Drugs
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Cesare Ernesto Maria Gruber, Marzia Montalbano, Gianpiero D'Offizi, Martina Rueca, Andrea Antinori, Chiara Taibi, Maria Rosaria Capobianchi, Claudia Minosse, Mauro Zaccarelli, Anna Rosa Garbuglia, Fiona McPhee, and Elisabetta Grilli
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Male ,0301 basic medicine ,hepatitis C virus ,viruses ,Hepacivirus ,medicine.disease_cause ,chemistry.chemical_compound ,0302 clinical medicine ,Recurrence ,Medicine ,Phylogeny ,HCV late relapse ,education.field_of_study ,High-Throughput Nucleotide Sequencing ,virus diseases ,Middle Aged ,Hepatitis C ,QR1-502 ,Phenotype ,Treatment Outcome ,Infectious Diseases ,NGS ,HCV ,RNA, Viral ,Female ,030211 gastroenterology & hepatology ,Late Relapse ,Direct acting ,HCV reinfection ,Genotype ,Hepatitis C virus ,Population ,Viral quasispecies ,Antiviral Agents ,Microbiology ,Article ,Viral Relapse ,03 medical and health sciences ,Virology ,Humans ,In patient ,Amino Acid Sequence ,education ,NS5B ,Base Sequence ,business.industry ,digestive system diseases ,030104 developmental biology ,chemistry ,Reinfection ,next-generation sequencing ,phylogenetic ,business - Abstract
The risk of hepatitis C virus (HCV) recurrence after direct-acting antiviral (DAA) treatment is <, 0.5%. However, the distinction between HCV RNA late relapse and reinfection still represents a challenge in virological diagnostics. The aim of this study was to employ next-generation sequencing (NGS) to investigate HCV RNA recurrence in patients achieving a sustained virologic response (SVR) at least six months post-treatment. NGS was performed on plasma samples from six HCV-positive patients (Pt1–6) treated with DAA. NGS of HCV NS5B was analyzed before treatment (T0), after HCV RNA rebound (T1), and, for Pt3, after a second rebound (T2). Reinfection was confirmed for Pt5, and for the first rebound observed in Pt3. Conversely, viral relapse was observed when comparing T0 and T1 for Pt6 and T1 and T2 for Pt3. Z-scores were calculated and used to predict whether HCV-positive patient samples at different time points belonged to the same quasispecies population. A low Z-score of <, 2.58 confirmed that viral quasispecies detected at T0 and T1 were closely related for both Pt1 and Pt2, while the Z-score for Pt4 was suggestive of possible reinfection. NGS data analyses indicate that the Z-score may be a useful parameter for distinguishing late relapse from reinfection.
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- 2021
8. The newly introduced SARS-CoV-2 variant A222V is rapidly spreading in Lazio region, Italy
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Cesare Ernesto Maria Gruber, Antonino Di Caro, Emanuela Giombini, Martina Rueca, Francesco Messina, Barbara Bartolini, Giuseppe Ippolito, and Maria Rosaria Capobianchi
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2019-20 coronavirus outbreak ,Geography ,Lazio region ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Clade ,Virology - Abstract
A new SARS-CoV-2 clade (GV) characterized by S substitution A222V, first reported from Spain in March, is rapidly spreading across Europe. To establish the A222V variant involvement in the infection rise in Italy, all GISAID sequences from Italy and those from our Laboratory (Lazio) in the period June-October were analysed. A222V, first recognized in August, represents 11.2% of sequences in this period, reaching 100% of autochthonous sequences in October, supporting increased GV circulation in Italy.
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- 2020
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9. SARS-CoV-2 Early Screening at the Point of Entry: Travelers From Bangladesh to Italy-July 2020
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Cesare Ernesto Maria Gruber, Antonino Di Caro, Barbara Bartolini, Emanuela Giombini, Martina Rueca, Francesco Messina, Maria Rosaria Capobianchi, Simone Lanini, Francesco Vairo, Eleonora Lalle, and Maria Beatrice Valli
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0301 basic medicine ,2019-20 coronavirus outbreak ,Point of entry ,Coronavirus disease 2019 (COVID-19) ,lcsh:QH426-470 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,030106 microbiology ,Biology ,molecular epidemiology ,03 medical and health sciences ,Genetics ,next generation genome sequencing ,Genetics (clinical) ,Phylogenetic tree ,Molecular epidemiology ,SARS-CoV-2 ,phylogenetic analysis ,fungi ,COVID-19 ,early detection at point of entry ,Brief Research Report ,mutations ,Virology ,Mutational analysis ,lcsh:Genetics ,030104 developmental biology ,Molecular Medicine - Abstract
We report phylogenetic and mutational analysis by NGS of six SARS-CoV-2 strains from patients flying from Bangladesh to Italy (July 2020). Data suggest that no further circulation of such imported strains occurred in Italy, stating the efficacy of early screening at the point of entry and supporting the importance of molecular epidemiology in monitoring the efficacy of control measures.
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- 2020
10. Chikungunya Outbreak in the Republic of the Congo, 2019-Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation
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Fabrizio Carletti, Martina Rueca, Martin Parfait Aimè Coussoud-Mavoungou, Francesca Colavita, Maria Rosaria Capobianchi, Chiara Montaldo, Emanuela Giombini, Richard Kock, Najmul Haider, Cesare Ernesto Maria Gruber, Antonino Di Caro, Jacqueline Lydia Mikolo, Beatriz Escudero-Pérez, Concetta Castilletti, Vincent J. Munster, Stephanie N. Seifert, Biez Ulrich Judicaël, Emily V Nelson, Leonard E. G. Mboera, César Muñoz-Fontela, Vincenzo Puro, Robert J. Fischer, Francesco Vairo, Patrick K. Tungu, Francesco Messina, Francine Ntoumi, Emanuele Nicastri, Lambert Kitembo, Steve Diafouka-Diatela, Marco Iannetta, Barbara Bartolini, Giuseppe Ippolito, Alimuddin Zumla, Chantal Portella, Sergio Gómez-Medina, and Simone Lanini
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0301 basic medicine ,Male ,chikungunya ,Republic of Congo ,lcsh:QR1-502 ,medicine.disease_cause ,lcsh:Microbiology ,Disease Outbreaks ,0302 clinical medicine ,Aedes ,Chikungunya ,Aedes spp ,Child ,Phylogeny ,Phylogenetic tree ,virus diseases ,Middle Aged ,Infectious Diseases ,Congo ,Child, Preschool ,Larva ,Enzootic ,Sylvatic cycle ,Female ,Chikungunya virus ,Adult ,Adolescent ,030231 tropical medicine ,mosquito ,Mosquito Vectors ,Biology ,Arbovirus ,Article ,03 medical and health sciences ,Young Adult ,Virology ,medicine ,Animals ,Humans ,outbreak ,Outbreak ,Bayes Theorem ,medicine.disease ,biology.organism_classification ,Settore MED/17 ,030104 developmental biology ,arbovirus ,Vector (epidemiology) ,Mutation ,Chikungunya Fever ,ONE-HEALTH - Abstract
The Republic of Congo (RoC) declared a chikungunya (CHIK) outbreak on 9 February 2019. We conducted a ONE-Human-Animal HEALTH epidemiological, virological and entomological investigation. Methods: We collected national surveillance and epidemiological data. CHIK diagnosis was based on RT-PCR and CHIKV-specific antibodies. Full CHIKV genome sequences were obtained by Sanger and MinION approaches and Bayesian tree phylogenetic analysis was performed. Mosquito larvae and 215 adult mosquitoes were collected in different villages of Kouilou and Pointe-Noire districts and estimates of Aedes (Ae.) mosquitos’ CHIKV-infectious bites obtained. We found two new CHIKV sequences of the East/Central/South African (ECSA) lineage, clustering with the recent enzootic sub-clade 2, showing the A226V mutation. The RoC 2019 CHIKV strain has two novel mutations, E2-T126M and E2-H351N. Phylogenetic suggests a common origin from 2016 Angola strain, from which it diverged around 1989 (95% HPD 1985–1994). The infectious bite pattern was similar for 2017, 2018 and early 2019. One Ae. albopictus pool was RT-PCR positive. The 2019 RoC CHIKV strain seems to be recently introduced or be endemic in sylvatic cycle. Distinct from the contemporary Indian CHIKV isolates and in contrast to the original Central-African strains (transmitted by Ae. aegypti), it carries the A226V mutation, indicating an independent adaptive mutation in response to vector replacement (Ae. albopictus vs Ae. aegypti).
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- 2020
11. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy
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Emanuele Nicastri, Francesca Colavita, Licia Bordi, Maria Rosaria Capobianchi, Concetta Castilletti, Emanuela Giombini, Fabrizio Carletti, Francesco Messina, Eleonora Lalle, Barbara Bartolini, Giuseppe Ippolito, Martina Rueca, Cesare Ernesto Maria Gruber, and Francesco Vairo
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Male ,Microbiology (medical) ,2019-20 coronavirus outbreak ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Pneumonia, Viral ,Genome, Viral ,Chlorocebus aethiops ,Cell Line ,Betacoronavirus ,Pandemic ,Animals ,Humans ,Base sequence ,Pandemics ,Vero Cells ,Phylogeny ,Base Sequence ,biology ,SARS-CoV-2 ,COVID-19 ,Genetic Variation ,General Medicine ,biology.organism_classification ,Virology ,Infectious Diseases ,Italy ,Vero cell ,Female ,Coronavirus Infections - Published
- 2020
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12. Fatal Outbreak in Tonkean Macaques Caused by Possibly Novel Orthopoxvirus, Italy, January 20151
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Goffredo Grifoni, Claudia Eleni, Vincenzo Puro, Giuseppe Manna, Lorenzo De Marco, Cesare Ernesto Maria Gruber, Antonino Di Caro, Francesca Rosone, Maria Teresa Scicluna, Giusy Cardeti, Fabrizio Carletti, Emanuela Giombini, Marina Selleri, Raniero Lorenzetti, Valentina Tagliapietra, Daniele Lapa, Maria Rosaria Capobianchi, Annapaola Rizzoli, Concetta Castilletti, and Gian Luca Autorino
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0301 basic medicine ,Microbiology (medical) ,Veterinary medicine ,education.field_of_study ,Epidemiology ,viruses ,Cowpox ,Population ,Outbreak ,Biology ,medicine.disease ,biology.organism_classification ,Virology ,Virus ,3. Good health ,Ectromelia ,03 medical and health sciences ,030104 developmental biology ,Infectious Diseases ,Immune system ,medicine ,Orthopoxvirus ,Clade ,education - Abstract
In January 2015, during a 3-week period, 12 captive Tonkean macacques at a sanctuary in Italy died. An orthopoxvirus infection was suspected because of negative-staining electron microscopy results. The diagnosis was confirmed by histology, virus isolation, and molecular analysis performed on different organs from all animals. An epidemiologic investigation was unable to define the infection source in the surrounding area. Trapped rodents were negative by virologic testing, but specific IgG was detected in 27.27% of small rodents and 14.28% of rats. An attenuated live vaccine was administered to the susceptible monkey population, and no adverse reactions were observed; a detectable humoral immune response was induced in most of the vaccinated animals. We performed molecular characterization of the orthopoxvirus isolate by next-generation sequencing. According to the phylogenetic analysis of the 9 conserved genes, the virus could be part of a novel clade, lying between cowpox and ectromelia viruses.
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- 2017
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13. Geographical Variability Affects CCHFV Detection by RT–PCR: A Tool for In-Silico Evaluation of Molecular Assays
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Marion Koopmans, Roland Grunow, Barbara Bartolini, Anna Papa, Ali Mirazimi, Giuseppe Ippolito, Roger Hewson, Concetta Castilletti, Tatjana Avšič, María P. Sánchez-Seco, Iva Christova, Maria Rosaria Capobianchi, Cesare Ernesto Maria Gruber, Antonino Di Caro, Chantal Reusken, Virology, Ministero della Salute (Italia), Unión Europea, European Centre for Disease Prevention and Control, and Unión Europea. Comisión Europea. H2020
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0301 basic medicine ,In silico ,030231 tropical medicine ,lcsh:QR1-502 ,Computational biology ,Biology ,emerging diseases ,Sensitivity and Specificity ,lcsh:Microbiology ,Article ,03 medical and health sciences ,0302 clinical medicine ,Virology ,Humans ,laboratory preparedness ,Computer Simulation ,Genetic variability ,ddc:610 ,arthropod-borne virus ,Pcr analysis ,Phylogeny ,Geography ,Reverse Transcriptase Polymerase Chain Reaction ,Arthropod-borne Virus ,Computational Biology ,Genetic Variation ,Crimean–Congo hemorrhagic fever virus ,Hemorrhagic fever virus ,3. Good health ,Geographic distribution ,molecular detection ,030104 developmental biology ,Infectious Diseases ,Real-time polymerase chain reaction ,CCHFV ,Molecular Diagnostic Techniques ,GenBank ,Hemorrhagic Fever Virus, Crimean-Congo ,Hemorrhagic Fever, Crimean ,610 Medizin und Gesundheit ,Software - Abstract
The Crimean&ndash, Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&, D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high genetic variability of CCHFV often hampers the efficacy of available molecular tests and can affect their diagnostic potential. Recently, increasing numbers of complete CCHFV genomic sequences have become available, allowing a better appreciation of the genomic evolution of this virus. We summarized the current knowledge on molecular methods and developed a new bioinformatics tool to evaluate the existing assays for CCHFV detection, with a special focus on strains circulating in different geographical areas. Twenty-two molecular methods and 181 sequences of CCHFV were collected, respectively, from PubMed and GenBank databases. Up to 28 mismatches between primers and probes of each assay and CCHFV strains were detected through in-silico PCR analysis. Combinations of up to three molecular methods markedly decreased the number of mismatches within most geographic areas. These results supported the good practice of CCHFV detection of performing more than one assay, aimed for different sequence targets. The choice of the most appropriate tests must take into account patient&rsquo, s travel history and geographic distribution of the different CCHFV strains.
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- 2019
14. Compartmentalized Replication of SARS-Cov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis
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Emanuela Giombini, Fausto Baldanti, Barbara Bartolini, Giuseppe Ippolito, Cesare Ernesto Maria Gruber, Antonino Di Caro, Luisa Marchioni, Antonio Piralla, Francesco Messina, Martina Rueca, and Maria Rosaria Capobianchi
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0301 basic medicine ,Microbiology (medical) ,030106 microbiology ,coronavirus ,SARS-COV-2 ,Viral quasispecies ,Biology ,Microbiology ,Genome ,Article ,DNA sequencing ,Nucleotide diversity ,03 medical and health sciences ,Virology ,Clade ,lcsh:QH301-705.5 ,Genetics ,variability ,Genetic heterogeneity ,COVID-19 ,quasispecies ,Ion semiconductor sequencing ,Amplicon ,3. Good health ,030104 developmental biology ,lcsh:Biology (General) - Abstract
We report whole-genome and intra-host variability of SARS-Cov-2 assessed by next generation sequencing (NGS) in upper (URT) and lower respiratory tract (LRT) from COVID-19 patients. The aim was to identify possible tissue-specific patterns and signatures of variant selection for each respiratory compartment. Six patients, admitted to the Intensive Care Unit, were included in the study. Thirteen URT and LRT were analyzed by NGS amplicon-based approach on Ion Torrent Platform. Bioinformatic analysis was performed using both realized in-house and supplied by ThermoFisher programs. Phylogenesis showed clade V clustering of the first patients diagnosed in Italy, and clade G for later strains. The presence of quasispecies was observed, with variants uniformly distributed along the genome and frequency of minority variants spanning from 1% to ~30%. For each patient, the patterns of variants in URT and LRT were profoundly different, indicating compartmentalized virus replication. No clear variant signature and no significant difference in nucleotide diversity between LRT and URT were observed. SARS-CoV-2 presents genetic heterogeneity and quasispecies compartmentalization in URT and LRT. Intra-patient diversity was low. The pattern of minority variants was highly heterogeneous and no specific district signature could be identified, nevertheless, analysis of samples, longitudinally collected in patients, supported quasispecies evolution.
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- 2020
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15. Whole Genome Characterization of Orthopoxvirus (OPV) Abatino, a Zoonotic Virus Representing a Putative Novel Clade of Old World Orthopoxviruses
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Gian Luca Autorino, Andreas Nitsche, Lorenzo De Marco, Alona Tyshaieva, Giuseppe Ippolito, Maria Rosaria Capobianchi, Raniero Lorenzetti, Fabrizio Carletti, Emanuela Giombini, Concetta Castilletti, Cesare Ernesto Maria Gruber, Andreas Andrusch, Giusy Cardeti, Marina Selleri, and Simon H. Tausch
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0301 basic medicine ,viruses ,030106 microbiology ,lcsh:QR1-502 ,cowpox virus ,orthopoxvirus ,Genome ,lcsh:Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Virology ,Orthopoxvirus ,ddc:610 ,phylogenetic tree ,Clade ,core gene set ,OPV Abatino ,biology ,Phylogenetic tree ,Ectromelia virus ,Cowpox virus ,ectromelia virus ,biology.organism_classification ,3. Good health ,030104 developmental biology ,Infectious Diseases ,chemistry ,Monkeypox virus ,Vaccinia ,610 Medizin und Gesundheit - Abstract
Orthopoxviruses (OPVs) are diffused over the complete Eurasian continent, but previously described strains are mostly from northern Europe, and few infections have been reported from Italy. Here we present the extended genomic characterization of OPV Abatino, a novel OPV isolated in Italy from an infected Tonkean macaque, with zoonotic potential. Phylogenetic analysis based on 102 conserved OPV genes (core gene set) showed that OPV Abatino is most closely related to the Ectromelia virus species (ECTV), although placed on a separate branch of the phylogenetic tree, bringing substantial support to the hypothesis that this strain may be part of a novel OPV clade. Extending the analysis to the entire set of genes (coding sequences, CDS) further substantiated this hypothesis. In fact the genome of OPV Abatino included more CDS than ECTV, most of the extra genes (mainly located in the terminal genome regions), showed the highest similarity with cowpox virus (CPXV), however vaccinia virus (VACV) and monkeypox virus (MPXV) were the closest OPV for certain CDS. These findings suggest that OPV Abatino could be the result of complex evolutionary events, diverging from any other previously described OPV, and may indicate that previously reported cases in Italy could represent the tip of the iceberg yet to be explored.
- Published
- 2018
16. Molecular characterization of the first Ebola virus isolated in Italy, from a health care worker repatriated from Sierra Leone
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Licia Bordi, Antonio Mazzarelli, Francesca Colavita, Daniele Lapa, Giuseppe Ippolito, Emanuele Nicastri, Nicola Petrosillo, Concetta Castilletti, Fabrizio Carletti, Alessandro Desideri, Eleonora Lalle, Alessio Valentini, Serena Quartu, Patrizia Marsella, Giovanni Chillemi, Roberta Chiappini, Silvia Meschi, Cesare Ernesto Maria Gruber, Antonino Di Caro, and Maria Rosaria Capobianchi
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0303 health sciences ,Ebola virus ,business.industry ,Settore BIO/11 ,viruses ,Biology ,medicine.disease_cause ,Virology ,3. Good health ,Sierra leone ,03 medical and health sciences ,0302 clinical medicine ,Viruses ,Health care ,Genetics ,medicine ,030212 general & internal medicine ,Clade ,business ,Molecular Biology ,Health worker ,030304 developmental biology - Abstract
Here, we report the complete genome sequence of an Ebola virus (EBOV) isolated from a health worker repatriated from Sierra Leone to Italy in November 2014. The sequence, clustering in clade 3 of the Sierra Leone sequences, was analyzed with respect to mutations possibly affecting diagnostic and therapeutic targets as well as virulence.
- Published
- 2015
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