1
|
D'Amato R, Taxiarchi C, Galardini M, Trusso A, Minuz RL, Grilli S, Somerville AGT, Shittu D, Khalil AS, Galizi R, Crisanti A, Simoni A, Müller R. Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages. Nat Commun 2024; 15:952. [PMID: 38296981 PMCID: PMC10830555 DOI: 10.1038/s41467-024-44907-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
CRISPR-based gene drives have the potential to spread within populations and are considered as promising vector control tools. A doublesex-targeting gene drive was able to suppress laboratory Anopheles mosquito populations in small and large cages, and it is considered for field application. Challenges related to the field-use of gene drives and the evolving regulatory framework suggest that systems able to modulate or revert the action of gene drives, could be part of post-release risk-mitigation plans. In this study, we challenge an AcrIIA4-based anti-drive to inhibit gene drive spread in age-structured Anopheles gambiae population under complex feeding and behavioural conditions. A stochastic model predicts the experimentally-observed genotype dynamics in age-structured populations in medium-sized cages and highlights the necessity of large-sized cage trials. These experiments and experimental-modelling framework demonstrate the effectiveness of the anti-drive in different scenarios, providing further corroboration for its use in controlling the spread of gene drive in Anopheles.
Collapse
Affiliation(s)
- Rocco D'Amato
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy
| | | | - Marco Galardini
- Biological Design Center, Boston University, Boston, MA, USA
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - Alessandro Trusso
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy
| | - Roxana L Minuz
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy
| | - Silvia Grilli
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Dammy Shittu
- Department of Life Sciences, Imperial College London, London, UK
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alekos Simoni
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
| | - Ruth Müller
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy.
- Unit of Entomology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
| |
Collapse
|
2
|
Angelini F, Rossi L, Taccogna S, Crisanti A, Borra G, Gozzi E. First report of Central-line-associated bloodstream infection (CLAB- SI) due to Enterococcus raffinosus (ER) in a cancer patient. Clin Ter 2023; 174:469-472. [PMID: 38048106 DOI: 10.7417/ct.2023.5010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Abstract Despite the advances made by therapeutic technologies, healthcare-associated infections (HAIs) are currently still a worldwide problem. Central-line-associated bloodstream infections (CLABSIs) are one of the most common causes of HAIs. The cost of CLABSIs is considerable, both for the increase in morbidity and financial resources expenses. Coagulase-negative staphylococci are the common pathogens responsible for CLABSIs, followed by Staphylococcus aureus, Enterococci, and Candida spp. The Enterococcus genus comprises of more than 50 species but E. faecalis and E. faecium are the most common causes of infections in humans. Enterococcus Raffinosus (ER) is a non-faecalis and non-faecium enterococcus even if ER has rarely been proven to be a human pathogen, recent reports of infections caused by enterococci that are relatively resistant to beta-lactam antibiotics by non-p-lactamase mechanisms have included strains of ER. Here we describe a first report of CLABSI due to Enterococcus Raffinosus in a cancer patient.
Collapse
Affiliation(s)
- F Angelini
- Medical Oncology Unit, Regina Apostolorum Hospital, Albano, Rome, Italy
| | - L Rossi
- UOC of Oncology, ASL Latina, Distretto 1, University of Rome "Sapienza" , Aprilia (LT), Italy
| | - S Taccogna
- Department of Pathology, Ospedale Regina Apostolorum, Albano, Rome, Italy
| | - A Crisanti
- Medical Laboratory, Regina Apostolorum Hospital, Albano, Rome, Italy
| | - G Borra
- Medical Laboratory, Regina Apostolorum Hospital, Albano, Rome, Italy
| | - E Gozzi
- Medical Oncology Unit, ASL RM6, Polo Ospedaliero di Anzio, Rome, Italy
| |
Collapse
|
3
|
Pondeville E, Failloux AB, Simard F, Volf P, Crisanti A, Haghighat-Khah RE, Busquets N, Abad FX, Wilson AJ, Bellini R, Marsh Arnaud S, Kohl A, Veronesi E. Infravec2 guidelines for the design and operation of containment level 2 and 3 insectaries in Europe. Pathog Glob Health 2023; 117:293-307. [PMID: 35996820 PMCID: PMC10081053 DOI: 10.1080/20477724.2022.2108639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
With the current expansion of vector-based research and an increasing number of facilities rearing arthropod vectors and infecting them with pathogens, common measures for containment of arthropods as well as manipulation of pathogens are becoming essential for the design and running of such research facilities to ensure safe work and reproducibility, without compromising experimental feasibility. These guidelines and comments were written by experts of the Infravec2 consortium, a Horizon 2020-funded consortium integrating the most sophisticated European infrastructures for research on arthropod vectors of human and animal diseases. They reflect current good practice across European laboratories with experience of safely handling different mosquito species and the pathogens they transmit. As such, they provide experience-based advice to assess and manage the risks to work safely with mosquitoes and the pathogens they transmit. This document can also form the basis for research with other arthropods, for example, midges, ticks or sandflies, with some modification to reflect specific requirements.
Collapse
Affiliation(s)
| | | | | | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Núria Busquets
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, Cerdanyola del Vallès, Spain
| | - Francesc Xavier Abad
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, Cerdanyola del Vallès, Spain
| | | | - Romeo Bellini
- Centro Agricoltura Ambiente “G.Nicoli”, Crevalcore, Italy
| | - Sarah Marsh Arnaud
- Institut Pasteur, Genetics and Genomics of Insect Vectors, Paris, France
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Eva Veronesi
- UZH, Institute of Parasitology, University of Zürich, Zürich, Switzerland
| |
Collapse
|
4
|
Abstract
Using the path integral representation of the nonequilibrium dynamics, we compute the most probable path between arbitrary starting and final points that is followed by an active particle driven by persistent noise. We focus our attention on the case of active particles immersed in harmonic potentials, where the trajectory can be computed analytically. Once we consider the extended Markovian dynamics where the self-propulsive drive evolves according to an Ornstein-Uhlenbeck process, we can compute the trajectory analytically with arbitrary conditions on position and self-propulsion velocity. We test the analytical predictions against numerical simulations and we compare the analytical results with those obtained within approximated equilibriumlike dynamics.
Collapse
Affiliation(s)
- Andrea Crisanti
- Dipartimento di Fisica, Sapienza Università di Roma Piazzale A. Moro 2, I-00185 Rome, Italy
| | - Matteo Paoluzzi
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, C. Martí Franquès 1, 08028 Barcelona, Spain
| |
Collapse
|
5
|
Pollegioni P, Persampieri T, Minuz RL, Bucci A, Trusso A, Martino SD, Leo C, Bruttini M, Ciolfi M, Waldvogel A, Tripet F, Simoni A, Crisanti A, Müller R. Introgression of a synthetic sex ratio distortion transgene into different genetic backgrounds of Anopheles coluzzii. Insect Mol Biol 2023; 32:56-68. [PMID: 36251429 PMCID: PMC10092091 DOI: 10.1111/imb.12813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The development of genetically modified mosquitoes (GMM) and their subsequent field release offers innovative approaches for vector control of malaria. A non-gene drive self-limiting male-bias Ag(PMB)1 strain has been developed in a 47-year-old laboratory G3 strain of Anopheles gambiae s.l. When Ag(PMB)1 males are crossed to wild-type females, expression of the endonuclease I-PpoI during spermatogenesis causes the meiotic cleavage of the X chromosome in sperm cells, leading to fertile offspring with a 95% male bias. However, World Health Organization states that the functionality of the transgene could differ when inserted in different genetic backgrounds of Anopheles coluzzii which is currently a predominant species in several West-African countries and thus a likely recipient for a potential release of self-limiting GMMs. In this study, we introgressed the transgene from the donor Ag(PMB)1 by six serial backcrosses into two recipient colonies of An. coluzzii that had been isolated in Mali and Burkina Faso. Scans of informative Single Nucleotide Polymorphism (SNP) markers and whole-genome sequencing analysis revealed a nearly complete introgression of chromosomes 3 and X, but a remarkable genomic divergence in a large region of chromosome 2 between the later backcrossed (BC6) transgenic offspring and the recipient paternal strains. These findings suggested to extend the backcrossing breeding strategy beyond BC6 generation and increasing the introgression efficiency of critical regions that have ecological and epidemiological implications through the targeted selection of specific markers. Disregarding differential introgression efficiency, we concluded that the phenotype of the sex ratio distorter is stable in the BC6 introgressed An. coluzzii strains.
Collapse
Affiliation(s)
- Paola Pollegioni
- Research Institute on Terrestrial EcosystemsNational Research CouncilTerniItaly
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Tania Persampieri
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Roxana L. Minuz
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Alessandro Bucci
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Alessandro Trusso
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Salvatore Di Martino
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Chiara Leo
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Marco Bruttini
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
- Tuscan Centre of Precision Medicine, Department of Medicine, Surgery and NeurosciencesUniversity of SienaSienaItaly
| | - Marco Ciolfi
- Research Institute on Terrestrial EcosystemsNational Research CouncilTerniItaly
| | | | - Frédéric Tripet
- Centre for Applied Entomology and ParasitologyKeele UniversityNewcastle‐under‐LymeUK
| | - Alekos Simoni
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Andrea Crisanti
- Department of Molecular MedicineUniversity of PadovaPadovaItaly
| | - Ruth Müller
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
- Unit Entomology, Department of Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
| |
Collapse
|
6
|
Morianou I, Crisanti A, Nolan T, Hammond AM. CRISPR-Mediated Cassette Exchange (CriMCE): A Method to Introduce and Isolate Precise Marker-Less Edits. CRISPR J 2022; 5:868-876. [PMID: 36378258 DOI: 10.1089/crispr.2022.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The introduction of small unmarked edits to the genome of insects is essential to study the molecular underpinnings of important biological traits, such as resistance to insecticides and genetic control strategies. Advances in CRISPR genome engineering have made this possible, but prohibitively laborious for most laboratories due to low rates of editing and the lack of a selectable marker. To facilitate the generation and isolation of precise marker-less edits we have developed a two-step method based on CRISPR-mediated cassette exchange (CriMCE) of a marked placeholder for a variant of interest. This strategy can be used to introduce a wider range of potential edits compared with previous approaches while consolidating the workflow. We present proof-of-principle that CriMCE is a powerful tool by engineering three single nucleotide polymorphism variants into the genome of Anopheles gambiae, with 5-41 × higher rates of editing than homology-directed repair or prime editing.
Collapse
Affiliation(s)
- Ioanna Morianou
- Department of Life Sciences, Imperial College London, London, United Kingdom; S.r.l., Terni, Italy
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom; S.r.l., Terni, Italy.,Department of Molecular Medicine, University of Padova, Padua, Italy; S.r.l., Terni, Italy
| | - Tony Nolan
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom; S.r.l., Terni, Italy
| | - Andrew M Hammond
- Department of Life Sciences, Imperial College London, London, United Kingdom; S.r.l., Terni, Italy.,Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA; and S.r.l., Terni, Italy.,Biocentis, S.r.l., Terni, Italy
| |
Collapse
|
7
|
Del Vecchio C, Cracknell Daniels B, Brancaccio G, Brazzale AR, Lavezzo E, Ciavarella C, Onelia F, Franchin E, Manuto L, Bianca F, Cianci V, Cattelan AM, Dorigatti I, Toppo S, Crisanti A. Impact of antigen test target failure and testing strategies on the transmission of SARS-CoV-2 variants. Nat Commun 2022; 13:5870. [PMID: 36198689 PMCID: PMC9533294 DOI: 10.1038/s41467-022-33460-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/15/2022] [Indexed: 11/09/2022] Open
Abstract
Population testing remains central to COVID-19 control and surveillance, with countries increasingly using antigen tests rather than molecular tests. Here we describe a SARS-CoV-2 variant that escapes N antigen tests due to multiple disruptive amino-acid substitutions in the N protein. By fitting a multistrain compartmental model to genomic and epidemiological data, we show that widespread antigen testing in the Italian region of Veneto favored the undetected spread of the antigen-escape variant compared to the rest of Italy. We highlight novel limitations of widespread antigen testing in the absence of molecular testing for diagnostic or confirmatory purposes. Notably, we find that genomic surveillance systems which rely on antigen population testing to identify samples for sequencing will bias detection of escape antigen test variants. Together, these findings highlight the importance of retaining molecular testing for surveillance purposes, including in contexts where the use of antigen tests is widespread.
Collapse
Affiliation(s)
- Claudia Del Vecchio
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy
| | - Bethan Cracknell Daniels
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Giuseppina Brancaccio
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy
| | | | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Francesco Onelia
- Microbiology and Virology Diagnostic Unit, Padua University Hospital, Via Giustiniani 2, Padua, 35128, Italy
| | - Elisa Franchin
- Microbiology and Virology Diagnostic Unit, Padua University Hospital, Via Giustiniani 2, Padua, 35128, Italy
| | - Laura Manuto
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy
| | - Federico Bianca
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy
| | - Vito Cianci
- ER Unit, Emergency-Urgency Department, Padua University Hospital, Via Giustiniani 2, Padua, 35128, Italy
| | - Anna Maria Cattelan
- Infectious and Tropical Diseases Unit, Padua University Hospital, Via Giustiniani 2, Padua, 35128, Italy
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, School of Public Health, Imperial College London, London, UK.
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy. .,CRIBI Biotech Center, University of Padua, V.le G. Colombo, 3, Padua, 35131, Italy.
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy. .,Microbiology and Virology Diagnostic Unit, Padua University Hospital, Via Giustiniani 2, Padua, 35128, Italy. .,Department of Life Science, Imperial College London, South Kensington Campus, Imperial College Road, SW7 AZ, London, UK.
| |
Collapse
|
8
|
Ferrari S, Franco E, Del Vecchio C, Zorzi I, Fasolo E, Crisanti A, Ponzin D. Presence of SARS-CoV-2 RNA in human corneal tissues donated in Italy during the COVID-19 pandemic. BMJ Open Ophthalmol 2022; 7:bmjophth-2022-000990. [PMID: 36161826 PMCID: PMC9189543 DOI: 10.1136/bmjophth-2022-000990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Objective To analyse corneal tissues from asymptomatic donors with a postmortem nasopharyngeal swab tested positive for the presence of SARS-CoV-2 RNA, and therefore, understand the role that corneal transplantation may have in viral transmission. Methods and analysis Between March 2020 and October 2021, 101 corneas (out of 8154 collected in Italy) from 51 donors (out of a total of 4155 Italian donors) positive for SARS-CoV-2 after postmortem nasopharyngeal swab tests were analysed for the presence of SARS-CoV-2 RNA through real-time RT-PCR. When available, the corneal tissue storage media were also assessed. Corneas and/or storage media with confirmed presence of SARS-CoV-2 RNA were further investigated by isolating SARS-CoV-2 virions, which were used to infect VeroE6 target cells. Results Only N=4 corneas and/or storage media out of 101 showed presence of SARS-CoV-2 RNA. No VeroE6 cell infection was detected with viral isolates, thus suggesting no presence of SARS-CoV-2 virions in corneal specimens and storage media. Conclusions The presence of SARS-CoV-2 in cornea specimens would seem to be more likely due to prolonged detection of RNA rather than to active viral replication, with very low risk of infectivity and transmission through keratoplasty.
Collapse
Affiliation(s)
| | - Elena Franco
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Istituto Internazionale per la Ricerca e Formazione in Oftalmologia (IRFO), Forlì, Italy
| | | | - Ilaria Zorzi
- Fondazione Banca degli Occhi del Veneto, Venice, Italy
| | - Elisa Fasolo
- Fondazione Banca degli Occhi del Veneto, Venice, Italy
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padua, Padova, Italy
| | - Diego Ponzin
- Fondazione Banca degli Occhi del Veneto, Venice, Italy
| |
Collapse
|
9
|
Gittelman RM, Lavezzo E, Snyder TM, Zahid HJ, Carty CL, Elyanow R, Dalai S, Kirsch I, Baldo L, Manuto L, Franchin E, Del Vecchio C, Pacenti M, Boldrin C, Cattai M, Saluzzo F, Padoan A, Plebani M, Simeoni F, Bordini J, Lorè NI, Lazarević D, Cirillo DM, Ghia P, Toppo S, Carlson JM, Robins HS, Crisanti A, Tonon G. Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection. JCI Insight 2022; 7:e151849. [PMID: 35439174 PMCID: PMC9220833 DOI: 10.1172/jci.insight.151849] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 04/13/2022] [Indexed: 11/22/2022] Open
Abstract
T cells play a prominent role in orchestrating the immune response to viral diseases, but their role in the clinical presentation and subsequent immunity to SARS-CoV-2 infection remains poorly understood. As part of a population-based survey of the municipality of Vo', Italy, conducted after the initial SARS-CoV-2 outbreak, we sampled the T cell receptor (TCR) repertoires of the population 2 months after the initial PCR survey and followed up positive cases 9 and 15 months later. At 2 months, we found that 97.0% (98 of 101) of cases had elevated levels of TCRs associated with SARS-CoV-2. T cell frequency (depth) was increased in individuals with more severe disease. Both depth and diversity (breadth) of the TCR repertoire were positively associated with neutralizing antibody titers, driven mostly by CD4+ T cells directed against spike protein. At the later time points, detection of these TCRs remained high, with 90.7% (78 of 96) and 86.2% (25 of 29) of individuals having detectable signal at 9 and 15 months, respectively. Forty-three individuals were vaccinated by month 15 and showed a significant increase in TCRs directed against spike protein. Taken together, these results demonstrate the central role of T cells in mounting an immune defense against SARS-CoV-2 that persists out to 15 months.
Collapse
Affiliation(s)
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | | | - Sudeb Dalai
- Adaptive Biotechnologies, Seattle, Washington, USA
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Ilan Kirsch
- Adaptive Biotechnologies, Seattle, Washington, USA
| | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington, USA
| | - Laura Manuto
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Monia Pacenti
- Azienda Ospedale Padova, Microbiology and Virology Unit, Padua, Italy
| | - Caterina Boldrin
- Azienda Ospedale Padova, Microbiology and Virology Unit, Padua, Italy
| | - Margherita Cattai
- Azienda Ospedale Padova, Microbiology and Virology Unit, Padua, Italy
| | - Francesca Saluzzo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Andrea Padoan
- Department of Medicine, University of Padova, Padua, Italy
| | - Mario Plebani
- Department of Medicine, University of Padova, Padua, Italy
| | | | - Jessica Bordini
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Nicola I. Lorè
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Daniela M. Cirillo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Paolo Ghia
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | | | | | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Giovanni Tonon
- Center for Omics Sciences and
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| |
Collapse
|
10
|
Lai A, Bergna A, Toppo S, Morganti M, Menzo S, Ghisetti V, Bruzzone B, Codeluppi M, Fiore V, Rullo EV, Antonelli G, Sarmati L, Brindicci G, Callegaro A, Sagnelli C, Francisci D, Vicenti I, Miola A, Tonon G, Cirillo D, Menozzi I, Caucci S, Cerutti F, Orsi A, Schiavo R, Babudieri S, Nunnari G, Mastroianni CM, Andreoni M, Monno L, Guarneri D, Coppola N, Crisanti A, Galli M, Zehender G. Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. Sci Rep 2022; 12:5736. [PMID: 35388091 PMCID: PMC8986836 DOI: 10.1038/s41598-022-09738-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/25/2022] [Indexed: 12/29/2022] Open
Abstract
The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including < 80 Italian isolates, while most of the Italian strains were intermixed in the whole tree. Pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 (20B) most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 (20D) developed most probably in other European countries entering Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.
Collapse
Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, University of Milan, Milan, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy.,CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marina Morganti
- Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy
| | - Valeria Ghisetti
- Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino, Torino, Italy
| | | | - Mauro Codeluppi
- UOC of Infectious Diseases, Department of Oncology and Hematology, Guglielmo da Saliceto Hospital, AUSL Piacenza, Piacenza, Italy
| | - Vito Fiore
- Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Emmanuele Venanzi Rullo
- Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina, Messina, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | | | | | - Annapaola Callegaro
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, "Santa Maria della Misericordia" Hospital, University of Perugia, Perugia, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Arianna Miola
- Intesa San Paolo Innovation Center-AI LAB, Turin, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS Ospedale San Raffaele, Milan, Italy.,Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Daniela Cirillo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ilaria Menozzi
- Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Sara Caucci
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy
| | - Francesco Cerutti
- Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino, Torino, Italy
| | - Andrea Orsi
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Roberta Schiavo
- UOC of Microbiology, Department of Clinical Pathology, Guglielmo da Saliceto Hospital, AUSL Piacenza, Piacenza, Italy
| | - Sergio Babudieri
- Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina, Messina, Italy
| | - Claudio M Mastroianni
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | | | - Laura Monno
- Infectious Diseases Unit, University of Bari, Bari, Italy
| | - Davide Guarneri
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Andrea Crisanti
- Microbiology and Virology Diagnostic Unit, Padua University Hospital, Padua, Italy.,Department of Life Science, Imperial College London, South Kensington Campus Imperial College Road, London, SW7 AZ, UK
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy. .,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, University of Milan, Milan, Italy. .,CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milan, Italy.
| | | |
Collapse
|
11
|
Paoluzzi M, Gnan N, Grassi F, Salvetti M, Vanacore N, Crisanti A. A single-agent extension of the SIR model describes the impact of mobility restrictions on the COVID-19 epidemic. Sci Rep 2021; 11:24467. [PMID: 34963680 PMCID: PMC8714823 DOI: 10.1038/s41598-021-03721-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 12/07/2021] [Indexed: 12/04/2022] Open
Abstract
Mobility restrictions are successfully used to contain the diffusion of epidemics. In this work we explore their effect on the epidemic growth by investigating an extension of the Susceptible-Infected-Removed (SIR) model in which individual mobility is taken into account. In the model individual agents move on a chessboard with a Lévy walk and, within each square, epidemic spreading follows the standard SIR model. These simple rules allow to reproduce the sub-exponential growth of the epidemic evolution observed during the Covid-19 epidemic waves in several countries and which cannot be captured by the standard SIR model. We show that we can tune the slowing-down of the epidemic spreading by changing the dynamics of the agents from Lévy to Brownian and we investigate how the interplay among different containment strategies mitigate the epidemic spreading. Finally we demonstrate that we can reproduce the epidemic evolution of the first and second COVID-19 waves in Italy using only 3 parameters, i.e , the infection rate, the removing rate, and the mobility in the country. We provide an estimate of the peak reduction due to imposed mobility restrictions, i. e., the so-called flattening the curve effect. Although based on few ingredients, the model captures the kinetic of the epidemic waves, returning mobility values that are consistent with a lock-down intervention during the first wave and milder limitations, associated to a weaker peak reduction, during the second wave.
Collapse
Affiliation(s)
- Matteo Paoluzzi
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, C. Martí Franquès 1, 08028, Barcelona, Spain.
| | - Nicoletta Gnan
- CNR-ISC, Institute for Complex Systems UOS "Sapienza", Piazzale A. Moro 2, 00185, Rome, Italy
- Department of Physics, Sapienza University of Rome, Rome, Italy
| | - Francesca Grassi
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Marco Salvetti
- Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy
- IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Italy
| | - Nicola Vanacore
- National Center for Disease Prevention and Health Promotion, Istituto Superiore di Sanità, Rome, Italy
| | - Andrea Crisanti
- CNR-ISC, Institute for Complex Systems UOS "Sapienza", Piazzale A. Moro 2, 00185, Rome, Italy
- Department of Physics, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
12
|
Ferrari S, Del Vecchio C, Leonardi A, Feltrin G, Yu AC, Busin M, Crisanti A, Ponzin D. Detection of severe acute respiratory syndrome coronavirus 2 in corneas from asymptomatic donors. Acta Ophthalmol 2021; 99:e1245-e1246. [PMID: 33326155 DOI: 10.1111/aos.14692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/04/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Stefano Ferrari
- Fondazione Banca degli Occhi del Veneto Zelarino‐Venice Italy
| | | | - Andrea Leonardi
- Department of Neuroscience, Ophthalmology Unit University of Padua Padova Italy
| | | | - Angeli Christy Yu
- Department of Morphology, Surgery and Experimental Medicine University of Ferrara Ferrara Italy
- Department of Ophthalmology Ospedali Privati Forlì “Villa Igea” Forlì Italy
- Istituto Internazionale per la Ricerca e Formazione in Oftalmologia Forlì Italy
| | - Massimo Busin
- Department of Morphology, Surgery and Experimental Medicine University of Ferrara Ferrara Italy
- Department of Ophthalmology Ospedali Privati Forlì “Villa Igea” Forlì Italy
- Istituto Internazionale per la Ricerca e Formazione in Oftalmologia Forlì Italy
| | - Andrea Crisanti
- Department of Molecular Medicine University of Padua Padua Italy
| | - Diego Ponzin
- Fondazione Banca degli Occhi del Veneto Zelarino‐Venice Italy
| |
Collapse
|
13
|
Pattaro C, Barbieri G, Foco L, Weichenberger CX, Biasiotto R, De Grandi A, Fuchsberger C, Egger C, Amon VSC, Hicks AA, Mian M, Mahlknecht A, Lombardo S, Meier H, Weiss H, Rainer R, Dejaco C, Weiss G, Lavezzo E, Crisanti A, Pizzato M, Domingues FS, Mascalzoni D, Gögele M, Melotti R, Pramstaller PP. Prospective epidemiological, molecular, and genetic characterization of a novel coronavirus disease in the Val Venosta/Vinschgau: the CHRIS COVID-19 study protocol. Pathog Glob Health 2021; 116:128-136. [PMID: 34637685 PMCID: PMC8515786 DOI: 10.1080/20477724.2021.1978225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The COVID-19 pandemic has been threatening the healthcare and socioeconomic systems of entire nations. While population-based surveys to assess the distribution of SARS-CoV-2 infection have become a priority, pre-existing longitudinal studies are ideally suited to assess the determinants of COVID-19 onset and severity.The Cooperative Health Research In South Tyrol (CHRIS) study completed the baseline recruitment of 13,393 adults from the Venosta/Vinschgau rural district in 2018, collecting extensive phenotypic and biomarker data, metabolomic data, densely imputed genotype and whole-exome sequencing data.Based on CHRIS, we designed a prospective study, called CHRIS COVID-19, aimed at: 1) estimating the incidence of SARS-CoV-2 infections; 2) screening for and investigating the determinants of incident infection among CHRIS participants and their household members; 3) monitoring the immune response of infected participants prospectively.An online screening questionnaire was sent to all CHRIS participants and their household members. A random sample of 1450 participants representative of the district population was invited to assess active (nasopharyngeal swab) or past (serum antibody test) infections. We prospectively invited for complete SARS-CoV-2 testing all questionnaire completers gauged as possible cases of past infection and their household members. In positive tested individuals, antibody response is monitored quarterly for one year. Untested and negative participants receive the screening questionnaire every four weeks until gauged as possible incident cases or till the study end.Originated from a collaboration between researchers and community stakeholders, the CHRIS COVID-19 study aims at generating knowledge about the epidemiological, molecular, and genetic characterization of COVID-19 and its long-term sequelae.
Collapse
Affiliation(s)
- Cristian Pattaro
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Giulia Barbieri
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Luisa Foco
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Christian X Weichenberger
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Roberta Biasiotto
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Alessandro De Grandi
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Christian Fuchsberger
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Clemens Egger
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Vera S C Amon
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Andrew A Hicks
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Michael Mian
- Department of Haematology, Hospital of Bolzano SABES-ASDAA, Bolzano, Italy.,College of Health-Care Professions, Claudiana, Bolzano, Italy
| | - Angelika Mahlknecht
- Institute of General Medicine, Provincial School of Health (Claudiana), Bolzano, Italy.,Institute of General Practice, Family Medicine and Preventive Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Stefano Lombardo
- Provincial Institute of Statistics (ASTAT), Administration of the Autonomous Province of Bolzano, Italy
| | - Horand Meier
- Clinical Governance Unit, Administration of the Autonomous Province of Bolzano, Italy
| | - Helmuth Weiss
- Hospital of Silandro, Healthcare System of the Autonomous Province of Bolzano, Italy
| | - Robert Rainer
- Hospital of Silandro, Healthcare System of the Autonomous Province of Bolzano, Italy
| | - Christian Dejaco
- Department of Rheumatology, Medical University Graz, Austria.,Department of Rheumatology, Hospital of Bruneck (SABES-ASDAA), Italy
| | - Günter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Italy
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Italy
| | - Massimo Pizzato
- Laboratory of Virus-Cell Interaction, Centre for Integrative Biology, University of Trento, Italy
| | - Francisco S Domingues
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Deborah Mascalzoni
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy.,Center for Research Ethics and Bioethics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala Sweden
| | - Martin Gögele
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Roberto Melotti
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| |
Collapse
|
14
|
Fuchs S, Garrood WT, Beber A, Hammond A, Galizi R, Gribble M, Morselli G, Hui TYJ, Willis K, Kranjc N, Burt A, Crisanti A, Nolan T. Resistance to a CRISPR-based gene drive at an evolutionarily conserved site is revealed by mimicking genotype fixation. PLoS Genet 2021; 17:e1009740. [PMID: 34610011 PMCID: PMC8519452 DOI: 10.1371/journal.pgen.1009740] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/15/2021] [Accepted: 09/24/2021] [Indexed: 01/06/2023] Open
Abstract
CRISPR-based homing gene drives can be designed to disrupt essential genes whilst biasing their own inheritance, leading to suppression of mosquito populations in the laboratory. This class of gene drives relies on CRISPR-Cas9 cleavage of a target sequence and copying ('homing') therein of the gene drive element from the homologous chromosome. However, target site mutations that are resistant to cleavage yet maintain the function of the essential gene are expected to be strongly selected for. Targeting functionally constrained regions where mutations are not easily tolerated should lower the probability of resistance. Evolutionary conservation at the sequence level is often a reliable indicator of functional constraint, though the actual level of underlying constraint between one conserved sequence and another can vary widely. Here we generated a novel adult lethal gene drive (ALGD) in the malaria vector Anopheles gambiae, targeting an ultra-conserved target site in a haplosufficient essential gene (AGAP029113) required during mosquito development, which fulfils many of the criteria for the target of a population suppression gene drive. We then designed a selection regime to experimentally assess the likelihood of generation and subsequent selection of gene drive resistant mutations at its target site. We simulated, in a caged population, a scenario where the gene drive was approaching fixation, where selection for resistance is expected to be strongest. Continuous sampling of the target locus revealed that a single, restorative, in-frame nucleotide substitution was selected. Our findings show that ultra-conservation alone need not be predictive of a site that is refractory to target site resistance. Our strategy to evaluate resistance in vivo could help to validate candidate gene drive targets for their resilience to resistance and help to improve predictions of the invasion dynamics of gene drives in field populations.
Collapse
Affiliation(s)
- Silke Fuchs
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - William T. Garrood
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Anna Beber
- Department of Biology, University of Padua, Padua, Italy
| | - Andrew Hammond
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, United States of America
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Matthew Gribble
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Giulia Morselli
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tin-Yu J. Hui
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Katie Willis
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Medicine, University of Padua, Padua, Italy
- * E-mail: (AC); (TN)
| | - Tony Nolan
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail: (AC); (TN)
| |
Collapse
|
15
|
Cocconcelli E, Castelli G, Onelia F, Lavezzo E, Giraudo C, Bernardinello N, Fichera G, Leoni D, Trevenzoli M, Saetta M, Cattelan A, Crisanti A, Spagnolo P, Balestro E. Disease Severity and Prognosis of SARS-CoV-2 Infection in Hospitalized Patients Is Not Associated With Viral Load in Nasopharyngeal Swab. Front Med (Lausanne) 2021; 8:714221. [PMID: 34568371 PMCID: PMC8460755 DOI: 10.3389/fmed.2021.714221] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/16/2021] [Indexed: 01/10/2023] Open
Abstract
Background: The impact of viral burden on severity and prognosis of patients hospitalized for Coronavirus Disease 2019 (COVID-19) is still a matter of debate due to controversial results. Herein, we sought to assess viral load in the nasopharyngeal swab and its association with severity score indexes and prognostic parameters. Methods: We included 127 symptomatic patients and 21 asymptomatic subjects with a diagnosis of SARS-CoV-2 infection obtained by reverse transcription polymerase chain reaction and presence of cycle threshold. According to the level of care needed during hospitalization, the population was categorized as high-intensity (HIMC, n = 76) or low intensity medical care setting (LIMC, n = 51). Results: Viral load did not differ among asymptomatic, LIMC, and HIMC SARS-CoV-2 positive patients [4.4 (2.9-5.3) vs. 4.8 (3.6-6.1) vs. 4.6 (3.9-5.7) log10 copies/ml, respectively; p = 0.31]. Similar results were observed when asymptomatic individuals were compared to hospitalized patients [4.4 (2.9-5.3) vs. 4.68 (3.8-5.9) log10 copies/ml; p = 0.13]. When the study population was divided in High (HVL, n = 64) and Low Viral Load (LVL, n = 63) group no differences were observed in disease severity at diagnosis. Furthermore, LVL and HVL groups did not differ with regard to duration of hospital stay, number of bacterial co-infections, need for high-intensity medical care and number of deaths. The viral load was not an independent risk factor for HIMC in an adjusted multivariate regression model (OR: 1.59; 95% CI: 0.46-5.55, p = 0.46). Conclusions: Viral load at diagnosis is similar in asymptomatic and hospitalized patients and is not associated with either worse outcomes during hospitalization. SARS CoV-2 viral load might not be the right tool to assist clinicians in risk-stratifying hospitalized patients.
Collapse
Affiliation(s)
- Elisabetta Cocconcelli
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova and Padova City Hospital, Padova, Italy
| | - Gioele Castelli
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova and Padova City Hospital, Padova, Italy
| | - Francesco Onelia
- Department of Molecular Medicine, University of Padova and Padova City Hospital, Padova, Italy
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova and Padova City Hospital, Padova, Italy
| | - Chiara Giraudo
- Department of Medicine, Institute of Radiology, University of Padova and Padova City Hospital, Padova, Italy
| | - Nicol Bernardinello
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova and Padova City Hospital, Padova, Italy
| | - Giulia Fichera
- Department of Medicine, Institute of Radiology, University of Padova and Padova City Hospital, Padova, Italy
| | - Davide Leoni
- Division of Infectious and Tropical Diseases, University of Padova and Padova City Hospital, Padova, Italy
| | - Marco Trevenzoli
- Division of Infectious and Tropical Diseases, University of Padova and Padova City Hospital, Padova, Italy
| | - Marina Saetta
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova and Padova City Hospital, Padova, Italy
| | - Annamaria Cattelan
- Division of Infectious and Tropical Diseases, University of Padova and Padova City Hospital, Padova, Italy
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova and Padova City Hospital, Padova, Italy
| | - Paolo Spagnolo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova and Padova City Hospital, Padova, Italy
| | - Elisabetta Balestro
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova and Padova City Hospital, Padova, Italy
| |
Collapse
|
16
|
Dorigatti I, Lavezzo E, Manuto L, Ciavarella C, Pacenti M, Boldrin C, Cattai M, Saluzzo F, Franchin E, Del Vecchio C, Caldart F, Castelli G, Nicoletti M, Nieddu E, Salvadoretti E, Labella B, Fava L, Guglielmo S, Fascina M, Grazioli M, Alvisi G, Vanuzzo MC, Zupo T, Calandrin R, Lisi V, Rossi L, Castagliuolo I, Merigliano S, Unwin HJT, Plebani M, Padoan A, Brazzale AR, Toppo S, Ferguson NM, Donnelly CA, Crisanti A. SARS-CoV-2 antibody dynamics and transmission from community-wide serological testing in the Italian municipality of Vo'. Nat Commun 2021; 12:4383. [PMID: 34282139 PMCID: PMC8289856 DOI: 10.1038/s41467-021-24622-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/21/2021] [Indexed: 01/04/2023] Open
Abstract
In February and March 2020, two mass swab testing campaigns were conducted in Vo', Italy. In May 2020, we tested 86% of the Vo' population with three immuno-assays detecting antibodies against the spike and nucleocapsid antigens, a neutralisation assay and Polymerase Chain Reaction (PCR). Subjects testing positive to PCR in February/March or a serological assay in May were tested again in November. Here we report on the results of the analysis of the May and November surveys. We estimate a seroprevalence of 3.5% (95% Credible Interval (CrI): 2.8-4.3%) in May. In November, 98.8% (95% Confidence Interval (CI): 93.7-100.0%) of sera which tested positive in May still reacted against at least one antigen; 18.6% (95% CI: 11.0-28.5%) showed an increase of antibody or neutralisation reactivity from May. Analysis of the serostatus of the members of 1,118 households indicates a 26.0% (95% CrI: 17.2-36.9%) Susceptible-Infectious Transmission Probability. Contact tracing had limited impact on epidemic suppression.
Collapse
Affiliation(s)
- Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK.
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padova, Italy.
| | - Laura Manuto
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | | | | | | | - Francesca Saluzzo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Federico Caldart
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gioele Castelli
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Michele Nicoletti
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Eleonora Nieddu
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Beatrice Labella
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Ludovico Fava
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Simone Guglielmo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Marco Grazioli
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gualtiero Alvisi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | | | | | | | | | | | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Mario Plebani
- Department of Medicine, University of Padova, Padova, Italy
| | - Andrea Padoan
- Department of Medicine, University of Padova, Padova, Italy
| | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padova, Italy
- CRIBI Biotech Centre, University of Padova, Padova, Italy
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padova, Italy.
- Azienda Ospedale Padova, Padova, Italy.
- Department of Life Science Imperial College London, Exhibition Road, London, UK.
| |
Collapse
|
17
|
Garrood WT, Kranjc N, Petri K, Kim DY, Guo JA, Hammond AM, Morianou I, Pattanayak V, Joung JK, Crisanti A, Simoni A. Analysis of off-target effects in CRISPR-based gene drives in the human malaria mosquito. Proc Natl Acad Sci U S A 2021; 118:e2004838117. [PMID: 34050017 PMCID: PMC8179207 DOI: 10.1073/pnas.2004838117] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 nuclease-based gene drives have been developed toward the aim of control of the human malaria vector Anopheles gambiae Gene drives are based on an active source of Cas9 nuclease in the germline that promotes super-Mendelian inheritance of the transgene by homology-directed repair ("homing"). Understanding whether CRISPR-induced off-target mutations are generated in Anopheles mosquitoes is an important aspect of risk assessment before any potential field release of this technology. We compared the frequencies and the propensity of off-target events to occur in four different gene-drive strains, including a deliberately promiscuous set-up, using a nongermline restricted promoter for SpCas9 and a guide RNA with many closely related sites (two or more mismatches) across the mosquito genome. Under this scenario we observed off-target mutations at frequencies no greater than 1.42%. We witnessed no evidence that CRISPR-induced off-target mutations were able to accumulate (or drive) in a mosquito population, despite multiple generations' exposure to the CRISPR-Cas9 nuclease construct. Furthermore, judicious design of the guide RNA used for homing of the CRISPR construct, combined with tight temporal constriction of Cas9 expression to the germline, rendered off-target mutations undetectable. The findings of this study represent an important milestone for the understanding and managing of CRISPR-Cas9 specificity in mosquitoes, and demonstrates that CRISPR off-target editing in the context of a mosquito gene drive can be reduced to minimal levels.
Collapse
Affiliation(s)
- William T Garrood
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Karl Petri
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Daniel Y Kim
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Jimmy A Guo
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Andrew M Hammond
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins University, Baltimore, MD 21205
| | - Ioanna Morianou
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Vikram Pattanayak
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom;
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
| | - Alekos Simoni
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom;
- Polo d'Innovazione Genomica, Genetica, e Biologia, 05100 Terni, Italy
| |
Collapse
|
18
|
Unal MA, Bayrakdar F, Fusco L, Besbinar O, Shuck CE, Yalcin S, Erken MT, Ozkul A, Gurcan C, Panatli O, Summak GY, Gokce C, Orecchioni M, Gazzi A, Vitale F, Somers J, Demir E, Yildiz SS, Nazir H, Grivel JC, Bedognetti D, Crisanti A, Akcali KC, Gogotsi Y, Delogu LG, Yilmazer A. 2D MXenes with antiviral and immunomodulatory properties: A pilot study against SARS-CoV-2. Nano Today 2021; 38:101136. [PMID: 33753982 PMCID: PMC7969865 DOI: 10.1016/j.nantod.2021.101136] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/22/2021] [Accepted: 03/15/2021] [Indexed: 05/03/2023]
Abstract
Two-dimensional transition metal carbides/carbonitrides known as MXenes are rapidly growing as multimodal nanoplatforms in biomedicine. Here, taking SARS-CoV-2 as a model, we explored the antiviral properties and immune-profile of a large panel of four highly stable and well-characterized MXenes - Ti3C2Tx, Ta4C3T x , Mo2Ti2C3T x and Nb4C3T x . To start with antiviral assessment, we first selected and deeply analyzed four different SARS-CoV-2 genotypes, common in most countries and carrying the wild type or mutated spike protein. When inhibition of the viral infection was tested in vitro with four viral clades, Ti3C2T x in particular, was able to significantly reduce infection only in SARS-CoV-2/clade GR infected Vero E6 cells. This difference in the antiviral activity, among the four viral particles tested, highlights the importance of considering the viral genotypes and mutations while testing antiviral activity of potential drugs and nanomaterials. Among the other MXenes tested, Mo2Ti2C3T x also showed antiviral properties. Proteomic, functional annotation analysis and comparison to the already published SARS-CoV-2 protein interaction map revealed that MXene-treatment exerts specific inhibitory mechanisms. Envisaging future antiviral MXene-based drug nano-formulations and considering the central importance of the immune response to viral infections, the immune impact of MXenes was evaluated on human primary immune cells by flow cytometry and single-cell mass cytometry on 17 distinct immune subpopulations. Moreover, 40 secreted cytokines were analyzed by Luminex technology. MXene immune profiling revealed i) the excellent bio and immune compatibility of the material, as well as the ability of MXene ii) to inhibit monocytes and iii) to reduce the release of pro-inflammatory cytokines, suggesting an anti-inflammatory effect elicited by MXene. We here report a selection of MXenes and viral SARS-CoV-2 genotypes/mutations, a series of the computational, structural and molecular data depicting deeply the SARS-CoV-2 mechanism of inhibition, as well as high dimensional single-cell immune-MXene profiling. Taken together, our results provide a compendium of knowledge for new developments of MXene-based multi-functioning nanosystems as antivirals and immune-modulators.
Collapse
Affiliation(s)
| | - Fatma Bayrakdar
- Ministry of Health General Directorate of Public Health, Microbiology References Laboratory, Ankara, Turkey
| | - Laura Fusco
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Cancer Research Department, Sidra Medicine, Doha, Qatar
| | - Omur Besbinar
- Stem Cell Institute, Ankara University, Balgat, Ankara, Turkey
- Department of Biomedical Engineering, Ankara University, Golbasi, Ankara, Turkey
| | - Christopher E Shuck
- A.J. Drexel Nanomaterials Institute and Department of Materials Science and Engineering, Drexel University, Philadelphia, PA, USA
| | - Süleyman Yalcin
- Ministry of Health General Directorate of Public Health, Microbiology References Laboratory, Ankara, Turkey
| | | | - Aykut Ozkul
- Department of Virology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Cansu Gurcan
- Stem Cell Institute, Ankara University, Balgat, Ankara, Turkey
- Department of Biomedical Engineering, Ankara University, Golbasi, Ankara, Turkey
| | - Oguzhan Panatli
- Department of Biomedical Engineering, Ankara University, Golbasi, Ankara, Turkey
| | | | - Cemile Gokce
- Department of Biomedical Engineering, Ankara University, Golbasi, Ankara, Turkey
| | | | - Arianna Gazzi
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Flavia Vitale
- Department of Neurology, Bioengineering, Physical Medicine & Rehabilitation, Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia Somers
- Oregon Health & Sciences University, Department of Molecular and Medical Genetics, Portland, OR, USA
| | - Emek Demir
- Oregon Health & Sciences University, Department of Molecular and Medical Genetics, Portland, OR, USA
| | - Serap Suzuk Yildiz
- Ministry of Health General Directorate of Public Health, Microbiology References Laboratory, Ankara, Turkey
| | - Hasan Nazir
- Department of Chemistry, Ankara University, Tandogan, Ankara, Turkey
| | | | - Davide Bedognetti
- Cancer Research Department, Sidra Medicine, Doha, Qatar
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Andrea Crisanti
- Department of Molecular Medicine, Padua University Hospital, Padua, Italy
| | - Kamil Can Akcali
- Stem Cell Institute, Ankara University, Balgat, Ankara, Turkey
- Department of Biophysics, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Yury Gogotsi
- A.J. Drexel Nanomaterials Institute and Department of Materials Science and Engineering, Drexel University, Philadelphia, PA, USA
| | | | - Açelya Yilmazer
- Stem Cell Institute, Ankara University, Balgat, Ankara, Turkey
- Department of Biomedical Engineering, Ankara University, Golbasi, Ankara, Turkey
| |
Collapse
|
19
|
Lunardi F, Fortarezza F, Vedovelli L, Pezzuto F, Boscolo A, Rossato M, Vettor R, Cattelan AM, Del Vecchio C, Crisanti A, Navalesi P, Gregori D, Calabrese F. Lower Gene Expression of Angiotensin Converting Enzyme 2 Receptor in Lung Tissues of Smokers with COVID-19 Pneumonia. Biomolecules 2021; 11:796. [PMID: 34073591 PMCID: PMC8226817 DOI: 10.3390/biom11060796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/17/2021] [Accepted: 05/24/2021] [Indexed: 01/08/2023] Open
Abstract
Angiotensin-converting enzyme 2 (ACE-2) is the main cell entry receptor for severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2), thus playing a critical role in causing Coronavirus disease 2019 (COVID-19). The role of smoking habit in the susceptibility to infection is still controversial. In this study we correlated lung ACE-2 gene expression with several clinical/pathological data to explore susceptibility to infection. This is a retrospective observational study on 29 consecutive COVID-19 autopsies. SARS-CoV-2 genome and ACE-2 mRNA expression were evaluated by real-time polymerase chain reaction in lung tissue samples and correlated with several data with focus on smoking habit. Smoking was less frequent in high than low ACE-2 expressors (p = 0.014). A Bayesian regression also including age, gender, hypertension, and virus quantity confirmed that smoking was the most probable risk factor associated with low ACE-2 expression in the model. A direct relation was found between viral quantity and ACE-2 expression (p = 0.028). Finally, high ACE-2 expressors more frequently showed a prevalent pattern of vascular injury than low expressors (p = 0.049). In conclusion, ACE-2 levels were decreased in the lung tissue of smokers with severe COVID-19 pneumonia. These results point out complex biological interactions between SARS-CoV-2 and ACE-2 particularly concerning the aspect of smoking habit and need larger prospective case series and translational studies.
Collapse
Affiliation(s)
- Francesca Lunardi
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35128 Padova, Italy; (F.L.); (F.F.); (L.V.); (F.P.); (D.G.)
| | - Francesco Fortarezza
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35128 Padova, Italy; (F.L.); (F.F.); (L.V.); (F.P.); (D.G.)
| | - Luca Vedovelli
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35128 Padova, Italy; (F.L.); (F.F.); (L.V.); (F.P.); (D.G.)
| | - Federica Pezzuto
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35128 Padova, Italy; (F.L.); (F.F.); (L.V.); (F.P.); (D.G.)
| | - Annalisa Boscolo
- Department of Medicine, University of Padova Medical School, 35128 Padova, Italy; (A.B.); (M.R.); (R.V.); (A.M.C.); (P.N.)
| | - Marco Rossato
- Department of Medicine, University of Padova Medical School, 35128 Padova, Italy; (A.B.); (M.R.); (R.V.); (A.M.C.); (P.N.)
| | - Roberto Vettor
- Department of Medicine, University of Padova Medical School, 35128 Padova, Italy; (A.B.); (M.R.); (R.V.); (A.M.C.); (P.N.)
| | - Anna Maria Cattelan
- Department of Medicine, University of Padova Medical School, 35128 Padova, Italy; (A.B.); (M.R.); (R.V.); (A.M.C.); (P.N.)
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padova Medical School, 35121 Padova, Italy; (C.D.V.); (A.C.)
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova Medical School, 35121 Padova, Italy; (C.D.V.); (A.C.)
| | - Paolo Navalesi
- Department of Medicine, University of Padova Medical School, 35128 Padova, Italy; (A.B.); (M.R.); (R.V.); (A.M.C.); (P.N.)
| | - Dario Gregori
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35128 Padova, Italy; (F.L.); (F.F.); (L.V.); (F.P.); (D.G.)
| | - Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35128 Padova, Italy; (F.L.); (F.F.); (L.V.); (F.P.); (D.G.)
| |
Collapse
|
20
|
Abstract
Laryngopharyngeal reflux (LPR) is a common disease caused by the leaking beck of gastric material out of the esophagus. The main symptoms are dysphonia, dysphagia, and cough. There is an established use of proton pump inhibitors (PPI) in patients with suspected LPR in common practice. This habit is translated by the standard strategy to use PPI in treating patients with gastroesophageal reflux. However, PPI can not wholly inhibit all types of reflux and are burden by adverse effects. Alginate, a derivative from algae, is devoid of side effects and effectively counteracts gastric material reflux forming a foaming gel in the stomach. The current study enrolled 100 outpatients with LPR. Alginate treatment was administered for two months. Patients underwent four visits (at baseline and 15, 30, and 60 days after treatment). A visual analog scale assessed the perception of dysphonia, dysphagia, and cough. Alginate significantly (p<0.0001) reduced all parameters. Therefore, the current study demonstrated that magnesium alginate was effective and safe in LPR treatment.
Collapse
Affiliation(s)
- G Ciprandi
- Consultant allergist, Casa di Cura Villa Montallegro, Genoa, Italy
| | - V Damiani
- Medical Department, D.M.G. Italia, Pomezia, Italy
| | - F M Passali
- Department of Clinical Sciences and Translational Medicine, University of Tor Vergata, Rome, Italy
| | - A Crisanti
- Clinical Medicine Department, Regina Apostolorum Hospital, Albano Laziale, Rome, Italy
| | - G Motta
- ENT Clinic, University Vanvitelli, Naples, Italy
| | - D Passali
- International Federation ORL Societies (IFOS) Executive Board members Rome Italy
| |
Collapse
|
21
|
Abstract
We describe the early phases of a COVID-19 epidemic in two contiguous Italian regions, Lombardy and Veneto, which were heavily and simultaneously hit by SARS-CoV-2 in Italy but showed markedly different disease outcome in terms of case fatality rate, SARS-CoV-2-attributable mortality and hospitalization. We discuss data limitations together with similarities and differences of the regional context possibly affecting COVID-19 control in the two regions. We conclude that the better COVID-19 outcome in Veneto was due, at least in part, to the adoption of a strategy of active search of asymptomatic SARS-CoV-2 infections (Reasoned Mass Testing), instead of a strategy strictly based on the detection of symptomatic cases.
Collapse
Affiliation(s)
- Antonio Cassone
- Polo Di Innovazione Della Genomica, Genetica E Biologia, Università Di Siena,Siena, Italy
| | - Andrea Crisanti
- Department of Microbiology, University of Padova, Padova, Italy
| |
Collapse
|
22
|
Trivellin N, Buffolo M, Onelia F, Pizzolato A, Barbato M, Orlandi VT, Del Vecchio C, Dughiero F, Zanoni E, Meneghesso G, Crisanti A, Meneghini M. Inactivating SARS-CoV-2 Using 275 nm UV-C LEDs through a Spherical Irradiation Box: Design, Characterization and Validation. Materials (Basel) 2021; 14:ma14092315. [PMID: 33946929 PMCID: PMC8125165 DOI: 10.3390/ma14092315] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/02/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022]
Abstract
We report on the design, characterization and validation of a spherical irradiation system for inactivating SARS-CoV-2, based on UV-C 275 nm LEDs. The system is designed to maximize irradiation intensity and uniformity and can be used for irradiating a volume of 18 L. To this aim: (i) several commercially available LEDs have been acquired and analyzed; (ii) a complete optical study has been carried out in order to optimize the efficacy of the system; (iii) the resulting prototype has been characterized optically and tested for the inactivation of SARS-CoV-2 for different exposure times, doses and surface types; (iv) the result achieved and the efficacy of the prototype have been compared with similar devices based on different technologies. Results indicate that a 99.9% inactivation can be reached after 1 min of treatment with a dose of 83.1 J/m2.
Collapse
Affiliation(s)
- Nicola Trivellin
- Department of Industrial Engineering, University of Padova, Via Gradenigo 6A, 35131 Padova, Italy;
- Department of Information Engineering, University of Padova, Via Gradenigo 6B, 35131 Padova, Italy; (M.B.); (M.B.); (E.Z.); (G.M.); (M.M.)
- Correspondence:
| | - Matteo Buffolo
- Department of Information Engineering, University of Padova, Via Gradenigo 6B, 35131 Padova, Italy; (M.B.); (M.B.); (E.Z.); (G.M.); (M.M.)
| | - Francesco Onelia
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy; (F.O.); (C.D.V.); (A.C.)
| | | | - Marco Barbato
- Department of Information Engineering, University of Padova, Via Gradenigo 6B, 35131 Padova, Italy; (M.B.); (M.B.); (E.Z.); (G.M.); (M.M.)
- LightCube SRL, Viale Navigazione Interna 51, 35129, Padova, Italy;
| | | | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy; (F.O.); (C.D.V.); (A.C.)
| | - Fabrizio Dughiero
- Department of Industrial Engineering, University of Padova, Via Gradenigo 6A, 35131 Padova, Italy;
| | - Enrico Zanoni
- Department of Information Engineering, University of Padova, Via Gradenigo 6B, 35131 Padova, Italy; (M.B.); (M.B.); (E.Z.); (G.M.); (M.M.)
| | - Gaudenzio Meneghesso
- Department of Information Engineering, University of Padova, Via Gradenigo 6B, 35131 Padova, Italy; (M.B.); (M.B.); (E.Z.); (G.M.); (M.M.)
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy; (F.O.); (C.D.V.); (A.C.)
| | - Matteo Meneghini
- Department of Information Engineering, University of Padova, Via Gradenigo 6B, 35131 Padova, Italy; (M.B.); (M.B.); (E.Z.); (G.M.); (M.M.)
| |
Collapse
|
23
|
Maggi C, Paoluzzi M, Crisanti A, Zaccarelli E, Gnan N. Universality class of the motility-induced critical point in large scale off-lattice simulations of active particles. Soft Matter 2021; 17:3807-3812. [PMID: 33645615 DOI: 10.1039/d0sm02162h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We perform large-scale computer simulations of an off-lattice two-dimensional model of active particles undergoing a motility-induced phase separation (MIPS) to investigate the system's critical behaviour close to the critical point of the MIPS curve. By sampling steady-state configurations for large system sizes and performing finite size scaling analysis we provide exhaustive evidence that the critical behaviour of this active system belongs to the Ising universality class. In addition to the scaling observables that are also typical of passive systems, we study the critical behaviour of the kinetic temperature difference between the two active phases. This quantity, which is always zero in equilibrium, displays instead a critical behavior in the active system which is well described by the same exponent of the order parameter in agreement with mean-field theory.
Collapse
Affiliation(s)
- Claudio Maggi
- NANOTEC-CNR, Institute of Nanotechnology, Soft and Living Matter Laboratory -Piazzale A. Moro 2, I-00185, Roma, Italy. and Dipartimento di Fisica, Università di Roma "Sapienza", I-00185, Roma, Italy
| | - Matteo Paoluzzi
- Departamento de Fìsica de la Matèria Condensada, Universitat de Barcelona, C. MartìFranquès 1, 08028 Barcelona, Spain
| | - Andrea Crisanti
- Dipartimento di Fisica, Università di Roma "Sapienza", I-00185, Roma, Italy and CNR-ISC, Institute of Complex Systems, Roma, Italy.
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, Università di Roma "Sapienza", I-00185, Roma, Italy and CNR-ISC, Institute of Complex Systems, Roma, Italy.
| | - Nicoletta Gnan
- Dipartimento di Fisica, Università di Roma "Sapienza", I-00185, Roma, Italy and CNR-ISC, Institute of Complex Systems, Roma, Italy.
| |
Collapse
|
24
|
Calabrese F, Pezzuto F, Giraudo C, Vedovelli L, Fortarezza F, Del Vecchio C, Lunardi F, Fraia AS, Cocconcelli E, Vuljan SE, Gregori D, Crisanti A, Balestro E, Spagnolo P. The Diagnostic Yield of the Multidisciplinary Discussion in Patients With COVID-19 Pneumonia. Front Med (Lausanne) 2021; 8:637872. [PMID: 33869252 PMCID: PMC8047147 DOI: 10.3389/fmed.2021.637872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/03/2021] [Indexed: 12/21/2022] Open
Abstract
Purpose: The hypothesis of the study was that a multidisciplinary approach involving experienced specialists in diffuse parenchymal lung disease might improve the diagnosis of patients with COVID-19 pneumonia. Methods: Two pulmonologists, two radiologists, and two pathologists reviewed 27 patients affected by severe COVID-19 pneumonia as the main diagnosis made by non-pulmonologists. To evaluate whether the contribution of specialists, individually and/or in combination, might modify the original diagnosis, a three-step virtual process was planned. The whole lung examination was considered the gold standard for the final diagnosis. The probability of a correct diagnosis was calculated using a model based on generalized estimating equations. The effectiveness of a multidisciplinary diagnosis was obtained by comparing diagnoses made by experienced pulmonologists with those made by non-pulmonologists. Results: In 19% of cases, the diagnosis of COVID-19-related death was mainly incorrect. The probability of a correct diagnosis increased strikingly from an undedicated clinician to an expert specialist. Every single specialist made significantly more correct diagnoses than any non-pulmonologist. The highest level of accuracy was achieved by the combination of 3 expert specialists (p = 0.0003). Conclusion: The dynamic interaction between expert specialists may significantly improve the diagnostic confidence and management of patients with COVID-19 pneumonia.
Collapse
Affiliation(s)
- Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Medical School, Padova, Italy
| | - Federica Pezzuto
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Medical School, Padova, Italy
| | - Chiara Giraudo
- Department of Medicine, University of Padova, Medical School, Padova, Italy
| | - Luca Vedovelli
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Medical School, Padova, Italy
| | - Francesco Fortarezza
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Medical School, Padova, Italy
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padova, Medical School, Padova, Italy
| | - Francesca Lunardi
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Medical School, Padova, Italy
| | - Anna Sara Fraia
- Department of Medicine, University of Padova, Medical School, Padova, Italy
| | - Elisabetta Cocconcelli
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Medical School, Padova, Italy
| | - Stefania Edith Vuljan
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Medical School, Padova, Italy
| | - Dario Gregori
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Medical School, Padova, Italy
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Medical School, Padova, Italy
| | - Elisabetta Balestro
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Medical School, Padova, Italy
| | - Paolo Spagnolo
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Medical School, Padova, Italy
| |
Collapse
|
25
|
Calabrese F, Pezzuto F, Fortarezza F, Boscolo A, Lunardi F, Giraudo C, Cattelan A, Del Vecchio C, Lorenzoni G, Vedovelli L, Sella N, Rossato M, Rea F, Vettor R, Plebani M, Cozzi E, Crisanti A, Navalesi P, Gregori D. Machine learning-based analysis of alveolar and vascular injury in SARS-CoV-2 acute respiratory failure. J Pathol 2021; 254:173-184. [PMID: 33626204 PMCID: PMC8014445 DOI: 10.1002/path.5653] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pneumopathy is characterized by a complex clinical picture and heterogeneous pathological lesions, both involving alveolar and vascular components. The severity and distribution of morphological lesions associated with SARS-CoV-2 and how they relate to clinical, laboratory, and radiological data have not yet been studied systematically. The main goals of the present study were to objectively identify pathological phenotypes and factors that, in addition to SARS-CoV-2, may influence their occurrence. Lungs from 26 patients who died from SARS-CoV-2 acute respiratory failure were comprehensively analysed. Robust machine learning techniques were implemented to obtain a global pathological score to distinguish phenotypes with prevalent vascular or alveolar injury. The score was then analysed to assess its possible correlation with clinical, laboratory, radiological, and tissue viral data. Furthermore, an exploratory random forest algorithm was developed to identify the most discriminative clinical characteristics at hospital admission that might predict pathological phenotypes of SARS-CoV-2. Vascular injury phenotype was observed in most cases being consistently present as pure form or in combination with alveolar injury. Phenotypes with more severe alveolar injury showed significantly more frequent tracheal intubation; longer invasive mechanical ventilation, illness duration, intensive care unit or hospital ward stay; and lower tissue viral quantity (p < 0.001). Furthermore, in this phenotype, superimposed infections, tumours, and aspiration pneumonia were also more frequent (p < 0.001). Random forest algorithm identified some clinical features at admission (body mass index, white blood cells, D-dimer, lymphocyte and platelet counts, fever, respiratory rate, and PaCO2 ) to stratify patients into different clinical clusters and potential pathological phenotypes (a web-app for score assessment has also been developed; https://r-ubesp.dctv.unipd.it/shiny/AVI-Score/). In SARS-CoV-2 positive patients, alveolar injury is often associated with other factors in addition to viral infection. Identifying phenotypical patterns at admission may enable a better stratification of patients, ultimately favouring the most appropriate management. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padua Medical School, Padua, Italy
| | - Federica Pezzuto
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padua Medical School, Padua, Italy
| | - Francesco Fortarezza
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padua Medical School, Padua, Italy
| | - Annalisa Boscolo
- Department of Medicine, University of Padua Medical School, Padua, Italy
| | - Francesca Lunardi
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padua Medical School, Padua, Italy
| | - Chiara Giraudo
- Department of Medicine, University of Padua Medical School, Padua, Italy
| | - Annamaria Cattelan
- Department of Medicine, University of Padua Medical School, Padua, Italy
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padua Medical School, Padua, Italy
| | - Giulia Lorenzoni
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padua Medical School, Padua, Italy
| | - Luca Vedovelli
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padua Medical School, Padua, Italy
| | - Nicolò Sella
- Department of Medicine, University of Padua Medical School, Padua, Italy
| | - Marco Rossato
- Department of Medicine, University of Padua Medical School, Padua, Italy
| | - Federico Rea
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padua Medical School, Padua, Italy
| | - Roberto Vettor
- Department of Medicine, University of Padua Medical School, Padua, Italy
| | - Mario Plebani
- Department of Medicine, University of Padua Medical School, Padua, Italy
| | - Emanuele Cozzi
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padua Medical School, Padua, Italy
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padua Medical School, Padua, Italy
| | - Paolo Navalesi
- Department of Medicine, University of Padua Medical School, Padua, Italy
| | - Dario Gregori
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padua Medical School, Padua, Italy
| |
Collapse
|
26
|
O'Loughlin SM, Forster AJ, Fuchs S, Dottorini T, Nolan T, Crisanti A, Burt A. Ultra-conserved sequences in the genomes of highly diverse Anopheles mosquitoes, with implications for malaria vector control. G3 (Bethesda) 2021; 11:6175102. [PMID: 33730159 PMCID: PMC8495744 DOI: 10.1093/g3journal/jkab086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/08/2021] [Indexed: 12/30/2022]
Abstract
DNA sequences that are exactly conserved over long evolutionary time scales have been observed in a variety of taxa. Such sequences are likely under strong functional constraint and they have been useful in the field of comparative genomics for identifying genome regions with regulatory function. A potential new application for these ultra-conserved elements (UCEs) has emerged in the development of gene drives to control mosquito populations. Many gene drives work by recognizing and inserting at a specific target sequence in the genome, often imposing a reproductive load as a consequence. They can therefore select for target sequence variants that provide resistance to the drive. Focusing on highly conserved, highly constrained sequences lowers the probability that variant, gene drive-resistant alleles can be tolerated. Here, we search for conserved sequences of 18 bp and over in an alignment of 21 Anopheles genomes, spanning an evolutionary timescale of 100 million years, and characterize the resulting sequences according to their location and function. Over 8000 UCEs were found across the alignment, with a maximum length of 164 bp. Length-corrected gene ontology analysis revealed that genes containing Anopheles UCEs were over-represented in categories with structural or nucleotide-binding functions. Known insect transcription factor binding sites were found in 48% of intergenic Anopheles UCEs. When we looked at the genome sequences of 1142 wild-caught mosquitoes, we found that 15% of the Anopheles UCEs contained no polymorphisms. Our list of Anopheles UCEs should provide a valuable starting point for the selection and testing of new targets for gene-drive modification in the mosquitoes that transmit malaria.
Collapse
Affiliation(s)
- Samantha M O'Loughlin
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK
| | - Annie J Forster
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK
| | - Silke Fuchs
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, LE12 5RD, UK
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK.,Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK
| |
Collapse
|
27
|
Ferrari S, Del Vecchio C, Bosio L, Zorzi I, Crisanti A, Ponzin D. Absence of Severe Acute Respiratory Syndrome Coronavirus 2 RNA in Human Corneal Donor Tissues: Implications for Transplantation. Cornea 2021; 40:e3-e4. [PMID: 33264142 DOI: 10.1097/ico.0000000000002594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | | | | | - Ilaria Zorzi
- The Veneto Eye Bank Foundation, Venice, Italy; and
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Diego Ponzin
- The Veneto Eye Bank Foundation, Venice, Italy; and
| |
Collapse
|
28
|
Annas GJ, Beisel CL, Clement K, Crisanti A, Francis S, Galardini M, Galizi R, Grünewald J, Immobile G, Khalil AS, Müller R, Pattanayak V, Petri K, Paul L, Pinello L, Simoni A, Taxiarchi C, Joung JK. A Code of Ethics for Gene Drive Research. CRISPR J 2021; 4:19-24. [PMID: 33571044 PMCID: PMC7898401 DOI: 10.1089/crispr.2020.0096] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Gene drives hold promise for use in controlling insect vectors of diseases, agricultural pests, and for conservation of ecosystems against invasive species. At the same time, this technology comes with potential risks that include unknown downstream effects on entire ecosystems as well as the accidental or nefarious spread of organisms that carry the gene drive machinery. A code of ethics can be a useful tool for all parties involved in the development and regulation of gene drives and can be used to help ensure that a balanced analysis of risks, benefits, and values is taken into consideration in the interest of society and humanity. We have developed a code of ethics for gene drive research with the hope that this code will encourage the development of an international framework that includes ethical guidance of gene drive research and is incorporated into scientific practice by gaining broad agreement and adherence.
Collapse
Affiliation(s)
- George J Annas
- Center for Health Law, Ethics & Human Rights, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Chase L Beisel
- Helmholtz Institute of RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Kendell Clement
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom.,Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Stacy Francis
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marco Galardini
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, United Kingdom
| | - Julian Grünewald
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Greta Immobile
- Polo d'Innovazione Genomica Genetica e Biologia SCaRL, Siena, Italy
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Ruth Müller
- Polo d'Innovazione Genomica Genetica e Biologia SCaRL, Siena, Italy.,Unit Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Vikram Pattanayak
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Karl Petri
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ligi Paul
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alekos Simoni
- Polo d'Innovazione Genomica Genetica e Biologia SCaRL, Siena, Italy
| | | | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
29
|
Seccia R, Romano S, Salvetti M, Crisanti A, Palagi L, Grassi F. Machine Learning Use for Prognostic Purposes in Multiple Sclerosis. Life (Basel) 2021; 11:life11020122. [PMID: 33562572 PMCID: PMC7914671 DOI: 10.3390/life11020122] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/28/2022] Open
Abstract
The course of multiple sclerosis begins with a relapsing-remitting phase, which evolves into a secondarily progressive form over an extremely variable period, depending on many factors, each with a subtle influence. To date, no prognostic factors or risk score have been validated to predict disease course in single individuals. This is increasingly frustrating, since several treatments can prevent relapses and slow progression, even for a long time, although the possible adverse effects are relevant, in particular for the more effective drugs. An early prediction of disease course would allow differentiation of the treatment based on the expected aggressiveness of the disease, reserving high-impact therapies for patients at greater risk. To increase prognostic capacity, approaches based on machine learning (ML) algorithms are being attempted, given the failure of other approaches. Here we review recent studies that have used clinical data, alone or with other types of data, to derive prognostic models. Several algorithms that have been used and compared are described. Although no study has proposed a clinically usable model, knowledge is building up and in the future strong tools are likely to emerge.
Collapse
Affiliation(s)
- Ruggiero Seccia
- Department of Computer, Control and Management Engineering “Antonio Ruberti”, Sapienza University of Rome, 00185 Rome, Italy; (R.S.); (L.P.)
| | - Silvia Romano
- Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (S.R.); (M.S.)
| | - Marco Salvetti
- Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (S.R.); (M.S.)
- Mediterranean Neurological Institute Neuromed, 86077 Pozzilli, Italy
| | - Andrea Crisanti
- Department of Physics, Sapienza University of Rome, 00185 Rome, Italy;
| | - Laura Palagi
- Department of Computer, Control and Management Engineering “Antonio Ruberti”, Sapienza University of Rome, 00185 Rome, Italy; (R.S.); (L.P.)
| | - Francesca Grassi
- Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence:
| |
Collapse
|
30
|
Lavezzo E, Franchin E, Ciavarella C, Cuomo-Dannenburg G, Barzon L, Del Vecchio C, Rossi L, Manganelli R, Loregian A, Navarin N, Abate D, Sciro M, Merigliano S, De Canale E, Vanuzzo MC, Besutti V, Saluzzo F, Onelia F, Pacenti M, Parisi SG, Carretta G, Donato D, Flor L, Cocchio S, Masi G, Sperduti A, Cattarino L, Salvador R, Nicoletti M, Caldart F, Castelli G, Nieddu E, Labella B, Fava L, Drigo M, Gaythorpe KAM, Brazzale AR, Toppo S, Trevisan M, Baldo V, Donnelly CA, Ferguson NM, Dorigatti I, Crisanti A. Author Correction: Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'. Nature 2021; 590:E11. [PMID: 33452443 PMCID: PMC7810098 DOI: 10.1038/s41586-020-2956-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Nicolò Navarin
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Davide Abate
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | - Francesca Saluzzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Francesco Onelia
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Saverio G Parisi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Silvia Cocchio
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alessandro Sperduti
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Renato Salvador
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | | | | | - Ludovico Fava
- School of Medicine, University of Padova, Padua, Italy
| | - Matteo Drigo
- School of Medicine, University of Padova, Padua, Italy
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Vincenzo Baldo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
| |
Collapse
|
31
|
Hammond A, Karlsson X, Morianou I, Kyrou K, Beaghton A, Gribble M, Kranjc N, Galizi R, Burt A, Crisanti A, Nolan T. Regulating the expression of gene drives is key to increasing their invasive potential and the mitigation of resistance. PLoS Genet 2021; 17:e1009321. [PMID: 33513149 PMCID: PMC7886172 DOI: 10.1371/journal.pgen.1009321] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 02/16/2021] [Accepted: 12/22/2020] [Indexed: 12/27/2022] Open
Abstract
Homing-based gene drives use a germline source of nuclease to copy themselves at specific target sites in a genome and bias their inheritance. Such gene drives can be designed to spread and deliberately suppress populations of malaria mosquitoes by impairing female fertility. However, strong unintended fitness costs of the drive and a propensity to generate resistant mutations can limit a gene drive’s potential to spread. Alternative germline regulatory sequences in the drive element confer improved fecundity of carrier individuals and reduced propensity for target site resistance. This is explained by reduced rates of end-joining repair of DNA breaks from parentally deposited nuclease in the embryo, which can produce heritable mutations that reduce gene drive penetrance. We tracked the generation and selection of resistant mutations over the course of a gene drive invasion of a population. Improved gene drives show faster invasion dynamics, increased suppressive effect and later onset of target site resistance. Our results show that regulation of nuclease expression is as important as the choice of target site when developing a robust homing-based gene drive for population suppression. Gene drives are selfish genetic elements that are able to drastically bias their own inheritance. They can rapidly invade populations, even starting from a very low frequency. Recent advances have allowed the engineering of gene drives deliberately designed to spread genetic traits of choice into populations of malaria-transmitting mosquito species–for example traits that impair a mosquito’s ability to reproduce or its ability to transmit parasites. The class of gene drive in question uses a very precise cutting and copying mechanism, termed ‘homing’, that allows it to increase its numbers in the cells that go on to form sperm or eggs, thereby increasing the chances that a copy of the gene drive is transmitted to offspring. However, while this type of gene drive can rapidly invade a mosquito population, mosquitoes can also eventually become resistant to the gene drive in some cases. Here we show that restricting the cutting activity of the gene drive to the germline tissue is crucial to maintaining its potency and we illustrate how failure to restrict this activity can lead to the generation of mutations that can make mosquitoes resistant to the gene drive.
Collapse
Affiliation(s)
- Andrew Hammond
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Xenia Karlsson
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Ioanna Morianou
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrea Beaghton
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Matthew Gribble
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom
- University of Padova, Padova, Italy
- * E-mail: (AC); (TN)
| | - Tony Nolan
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail: (AC); (TN)
| |
Collapse
|
32
|
Kranjc N, Crisanti A, Nolan T, Bernardini F. Anopheles gambiae Genome Conservation as a Resource for Rational Gene Drive Target Site Selection. Insects 2021; 12:97. [PMID: 33498790 PMCID: PMC7911984 DOI: 10.3390/insects12020097] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022]
Abstract
The increase in molecular tools for the genetic engineering of insect pests and disease vectors, such as Anopheles mosquitoes that transmit malaria, has led to an unprecedented investigation of the genomic landscape of these organisms. The understanding of genome variability in wild mosquito populations is of primary importance for vector control strategies. This is particularly the case for gene drive systems, which look to introduce genetic traits into a population by targeting specific genomic regions. Gene drive targets with functional or structural constraints are highly desirable as they are less likely to tolerate mutations that prevent targeting by the gene drive and consequent failure of the technology. In this study we describe a bioinformatic pipeline that allows the analysis of whole genome data for the identification of highly conserved regions that can point at potential functional or structural constraints. The analysis was conducted across the genomes of 22 insect species separated by more than hundred million years of evolution and includes the observed genomic variation within field caught samples of Anopheles gambiae and Anopheles coluzzii, the two most dominant malaria vectors. This study offers insight into the level of conservation at a genome-wide scale as well as at per base-pair resolution. The results of this analysis are gathered in a data storage system that allows for flexible extraction and bioinformatic manipulation. Furthermore, it represents a valuable resource that could provide insight into population structure and dynamics of the species in the complex and benefit the development and implementation of genetic strategies to tackle malaria.
Collapse
Affiliation(s)
- Nace Kranjc
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; (N.K.); (A.C.)
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; (N.K.); (A.C.)
| | - Tony Nolan
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Federica Bernardini
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; (N.K.); (A.C.)
| |
Collapse
|
33
|
Basso M, Zago D, De Canale E, Biasolo MA, Franchin E, Onelia F, Scaggiante R, Crisanti A, Parisi SG. 388. Multidrug Resistant Gram Negative Organisms Prevalence in Hospitalized Patients in an Italian Tertiary Level Hospital During COVID-19 Pandemia: First Detection is More Frequent in Clinical Samples than in Surveillance Rectal Swabs with Respect to the Previous 14-Month Period. Open Forum Infect Dis 2020. [PMCID: PMC7776132 DOI: 10.1093/ofid/ofaa439.583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
In Italy the pandemic of COVID-19 infection has placed an enormous burden on health authorities: contact precautions are required to avoid viral transmission and people should be subjected to standard infection control procedures. This is crucial in a country experiencing a high number of confirmed cases of COVID-19 infection in Europe and where multidrug-resistant Gram-negative bacteria (MDR-GN) are endemic.The aim of this study was to compare the prevalence of MDR-GN in surveillance rectal swabs (SRS) and in clinical samples (CS) in the period March 1,2020-April, 24 2020 with respect to the previous 2-month period and to the previous year.
Methods
The first SRS and the first CS with a MDR-GN isolate detected from 01/01/2019 to 24/04/2020 were included. Analysis was made by comparing three different study periods in 2019 and 2020 (Jan-Dec 2019, Jan-Feb 2020, and Mar-Apr 2020), for medical department, surgical department and intensive care department.
Results
Overall, 612 MDR-GN organisms were identified (399 SRS and 213 CS): carbapenemase-producing Klebsiella pneumoniae and Acinetobacter baumanii (CPAB) were the most frequently detected (Figure 1). We observed an increased relative frequency of patients with MDR-GN detected in CS respect to those found in SRS (32.7% vs 44.5% vs 70.6%, p=0.0005): 5/12 CS detected in the last period were isolated from the respiratory tract (Figure 2). Nine patients with COVID-19 pneumonia had MDR-GN. All but two patients had a previous negative SRS performed 4 days before (median value) and the median interval between COVID-19 positivity and MDR-GN positivity was 7 days.The six patients with CPAB isolation were all hospitalized in the same ward, with partially overlapping hospital stays during the study period. In 5 of them, CPAB was detected in the respiratory tract (Figure 3).
Conclusion
The first detection of MDR-GN in CS and the nosocomial MDR-GN acquisition despite cohorting due to COVID-19 infection underline the need to reinforce infection control measures in a high prevalence country during COVID-19 pandemia. A correct antimicrobial policy urged because, according to published data, most patients with COVID-19 infection received antimicrobial therapy: furthermore MDR-GN infection could play a role in the negative outcome of these patients.
Disclosures
All Authors: No reported disclosures
Collapse
Affiliation(s)
| | | | - Ettore De Canale
- Microbiology and Virology Unit - Padova Hopsital, Padova, Veneto, Italy
| | - Maria Angela Biasolo
- Department of Molecular Medicine, University of Padova, Padova, Padova, Veneto, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padova, Padova, Veneto, Italy
| | - Francesco Onelia
- Departmento of Molecular Medicine, University of Padova, Padova, Padova, Veneto, Italy
| | - Renzo Scaggiante
- Infectious Diseases Unit, Belluni Hospital, Belluno, Belluno, Veneto, Italy
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padova, Padova, Veneto, Italy
| | | |
Collapse
|
34
|
Affiliation(s)
- Luke S Alphey
- Arthropod Genetics Group, The Pirbright Institute, Woking GU24 0NF, United Kingdom
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London SW7 2BU, United Kingdom
- Department of Molecular Medicine, University of Padova, 35122 Padova, Italy
| | | | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| |
Collapse
|
35
|
Su MP, Georgiades M, Bagi J, Kyrou K, Crisanti A, Albert JT. Assessing the acoustic behaviour of Anopheles gambiae (s.l.) dsxF mutants: implications for vector control. Parasit Vectors 2020; 13:507. [PMID: 33028410 PMCID: PMC7539510 DOI: 10.1186/s13071-020-04382-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/28/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Release of gene-drive mutants to suppress Anopheles mosquito reproduction is a promising method of malaria control. However, many scientific, regulatory and ethical questions remain before transgenic mosquitoes can be utilised in the field. At a behavioural level, gene-drive carrying mutants should be at least as sexually attractive as the wildtype populations they compete against, with a key element of Anopheles copulation being acoustic courtship. We analysed sound emissions and acoustic preference in a doublesex mutant previously used to collapse Anopheles gambiae (s.l.) cages. METHODS Anopheles rely on flight tones produced by the beating of their wings for acoustic mating communication. We assessed the impact of disrupting a female-specific isoform of the doublesex gene (dsxF) on the wing beat frequency (WBF; measured as flight tone) of males (XY) and females (XX) in homozygous dsxF- mutants (dsxF-/-), heterozygous dsxF- carriers (dsxF+/-) and G3 dsxF+ controls (dsxF+/+). To exclude non-genetic influences, we controlled for temperature and wing length. We used a phonotaxis assay to test the acoustic preferences of mutant and control mosquitoes. RESULTS A previous study showed an altered phenotype only for dsxF-/- females, who appear intersex, suggesting that the female-specific dsxF allele is haplosufficient. We identified significant, dose-dependent increases in the WBF of both dsxF-/- and dsxF+/- females compared to dsxF+/+ females. All female WBFs remained significantly lower than male equivalents, though. Males showed stronger phonotactic responses to the WBFs of control dsxF+/+ females than to those of dsxF+/- and dsxF-/- females. We found no evidence of phonotaxis in any female genotype. No male genotypes displayed any deviations from controls. CONCLUSIONS A prerequisite for anopheline copulation is the phonotactic attraction of males towards female flight tones within mating swarms. Reductions in mutant acoustic attractiveness diminish their mating efficiency and thus the efficacy of population control efforts. Caged population assessments may not successfully reproduce natural mating scenarios. We propose to amend existing testing protocols to better reflect competition between mutants and target populations. Our findings confirm that dsxF disruption has no effect on males; for some phenotypic traits, such as female WBFs, the effects of dsxF appear dose-dependent rather than haplosufficient.
Collapse
Affiliation(s)
- Matthew P Su
- Ear Institute, University College London, 332 Grays Inn Road, London, WC1X 8EE, UK.,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Division of Biological Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Marcos Georgiades
- Ear Institute, University College London, 332 Grays Inn Road, London, WC1X 8EE, UK.,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Judit Bagi
- Ear Institute, University College London, 332 Grays Inn Road, London, WC1X 8EE, UK.,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, London, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK
| | - Joerg T Albert
- Ear Institute, University College London, 332 Grays Inn Road, London, WC1X 8EE, UK. .,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| |
Collapse
|
36
|
Pollegioni P, North AR, Persampieri T, Bucci A, Minuz RL, Groneberg DA, Nolan T, Papathanos P, Crisanti A, Müller R. Detecting the population dynamics of an autosomal sex ratio distorter transgene in malaria vector mosquitoes. J Appl Ecol 2020; 57:2086-2096. [PMID: 33149368 PMCID: PMC7594489 DOI: 10.1111/1365-2664.13702] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 06/09/2020] [Indexed: 11/28/2022]
Abstract
The development of genetically modified (GM) mosquitoes and their subsequent field release offers innovative and cost-effective approaches to reduce mosquito-borne diseases, such as malaria. A sex-distorting autosomal transgene has been developed recently in G3 mosquitoes, a laboratory strain of the malaria vector Anopheles gambiae s.l. The transgene expresses an endonuclease called I-PpoI during spermatogenesis, which selectively cleaves the X chromosome to result in ~95% male progeny. Following the World Health Organization guidance framework for the testing of GM mosquitoes, we assessed the dynamics of this transgene in large cages using a joint experimental modelling approach.We performed a 4-month experiment in large, indoor cages to study the population genetics of the transgene. The cages were set up to mimic a simple tropical environment with a diurnal light-cycle, constant temperature and constant humidity. We allowed the generations to overlap to engender a stable age structure in the populations. We constructed a model to mimic the experiments, and used the experimental data to infer the key model parameters.We identified two fitness costs associated with the transgene. First, transgenic adult males have reduced fertility and, second, their female progeny have reduced pupal survival rates. Our results demonstrate that the transgene is likely to disappear in <3 years under our confined conditions. Model predictions suggest this will be true over a wide range of background population sizes and transgene introduction rates. Synthesis and applications. Our study is in line with the World Health Organization guidance recommendations in regard to the development and testing of GM mosquitoes. Since the transgenic sex ratio distorter strain (Ag(PMB)1) has been considered for genetic vector control of malaria, we recorded the dynamics of this transgene in indoor-large cage populations and modelled its post-release persistence under different scenarios. We provide a demonstration of the self-limiting nature of the transgene, and identified new fitness costs that will further reduce the longevity of the transgene after its release. Finally, our study has showcased an alternative and effective statistical method for characterizing the phenotypic expression of a transgene in an insect pest population.
Collapse
Affiliation(s)
- Paola Pollegioni
- Polo d'Innovazione di GenomicaGenetica e Biologia Società Consortile R.L.TerniItaly
- National Research CouncilResearch Institute on Terrestrial EcosystemsPoranoItaly
| | - Ace R. North
- Department of ZoologyUniversity of OxfordOxfordUK
| | - Tania Persampieri
- Polo d'Innovazione di GenomicaGenetica e Biologia Società Consortile R.L.TerniItaly
| | - Alessandro Bucci
- Polo d'Innovazione di GenomicaGenetica e Biologia Società Consortile R.L.TerniItaly
| | - Roxana L. Minuz
- Polo d'Innovazione di GenomicaGenetica e Biologia Società Consortile R.L.TerniItaly
| | - David Alexander Groneberg
- Institute of Occupational Medicine, Social Medicine and Environmental MedicineGoethe University Frankfurt am MainFrankfurt am MainGermany
| | - Tony Nolan
- Department of Life SciencesImperial College LondonLondonUK
- Liverpool School of Tropical MedicineLiverpoolUK
| | - Philippos‐Aris Papathanos
- Department of Experimental MedicineUniversity of PerugiaPerugiaItaly
- Faculty of Agriculture, Food and EnvironmentHebrew University of JerusalemJerusalemIsrael
| | | | - Ruth Müller
- Polo d'Innovazione di GenomicaGenetica e Biologia Società Consortile R.L.TerniItaly
- Institute of Occupational Medicine, Social Medicine and Environmental MedicineGoethe University Frankfurt am MainFrankfurt am MainGermany
- Unit Medical EntomologyDepartment of Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
| |
Collapse
|
37
|
Cester G, Giraudo C, Causin F, Boemo DG, Anglani M, Capizzi A, Carretta G, Cattelan A, Cecchin D, Cianci V, Crisanti A, De Conti G, Donato D, Flor L, Gabrieli JD, Munari M, Navalesi P, Ponzoni A, Scapellato ML, Tiberio I, Vianello A, Stramare R. Retrospective Analysis of a Modified Organizational Model to Guarantee CT Workflow during the COVID-19 Outbreak in the Tertiary Hospital of Padova, Italy. J Clin Med 2020; 9:E3042. [PMID: 32967312 PMCID: PMC7563301 DOI: 10.3390/jcm9093042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/16/2020] [Indexed: 01/19/2023] Open
Abstract
At the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) outbreak in Italy, the cluster of Vò Euganeo was managed by the University Hospital of Padova. The Department of Diagnostic Imaging (DDI) conceived an organizational approach based on three different pathways for low-risk, high-risk, and confirmed Coronavirus Disease 19 (COVID-19) patients to accomplish three main targets: guarantee a safe pathway for non-COVID-19 patients, ensure health personnel safety, and maintain an efficient workload. Thus, an additional pathway was created with the aid of a trailer-mounted Computed Tomography (CT) scanner devoted to positive patients. We evaluated the performance of our approach from February 21 through April 12 in terms of workload (e.g., number of CT examinations) and safety (COVID-19-positive healthcare workers). There was an average of 72.2 and 17.8 COVID-19 patients per day in wards and the Intensive Care Unit (ICU), respectively. A total of 176 high-risk and positive patients were examined. High Resolution Computed Tomography (HRCT) was one of the most common exams, and 24 pulmonary embolism scans were performed. No in-hospital transmission occurred in the DDI neither among patients nor among health personnel. The weekly number of in-patient CT examinations decreased by 27.4%, and the surgical procedures decreased by 29.5%. Patient screening and dedicated diagnostic pathways allowed the maintenance of high standards of care while working in safety.
Collapse
Affiliation(s)
- Giacomo Cester
- Department of Diagnostic Imaging and Interventional Radiology, Neuroradiology, Padua University Hospital, 35128 Padua, Italy; (G.C.); (M.A.); (J.-D.G.)
| | - Chiara Giraudo
- Department of Medicine–DIMED, Institute of Radiology, Padua University Hospital, 35128 Padua, Italy; (C.G.); (R.S.)
| | - Francesco Causin
- Department of Diagnostic Imaging and Interventional Radiology, Neuroradiology, Padua University Hospital, 35128 Padua, Italy; (G.C.); (M.A.); (J.-D.G.)
| | - Deris Gianni Boemo
- Department of Directional Hospital Management, Padua University Hospital, 35128 Padova, Italy; (D.G.B.); (A.C.); (G.C.); (D.D.); (L.F.)
| | - Mariagiulia Anglani
- Department of Diagnostic Imaging and Interventional Radiology, Neuroradiology, Padua University Hospital, 35128 Padua, Italy; (G.C.); (M.A.); (J.-D.G.)
| | - Alfio Capizzi
- Department of Directional Hospital Management, Padua University Hospital, 35128 Padova, Italy; (D.G.B.); (A.C.); (G.C.); (D.D.); (L.F.)
| | - Giovanni Carretta
- Department of Directional Hospital Management, Padua University Hospital, 35128 Padova, Italy; (D.G.B.); (A.C.); (G.C.); (D.D.); (L.F.)
| | - Annamaria Cattelan
- Department of Internal Medicine, Infectious and Tropical Diseases, Padua University Hospital, 35128 Padua, Italy;
| | - Diego Cecchin
- Department of Medicine–DIMED, Nuclear Medicine Unit, Padua University Hospital, 35128 Padua, Italy;
| | - Vito Cianci
- ER Unit, Emergency-Urgency Department, Padua University Hospital, 35128 Padua, Italy;
| | - Andrea Crisanti
- Department of Molecular Medicine, Microbiology and Virology, Padua University Hospital, 35128 Padua, Italy;
| | - Giorgio De Conti
- Radiology Unit, Department of Diagnostic Imaging and Interventional Radiology, Padua University Hospital, 35128 Padua, Italy; (G.D.C.); (A.P.)
| | - Daniele Donato
- Department of Directional Hospital Management, Padua University Hospital, 35128 Padova, Italy; (D.G.B.); (A.C.); (G.C.); (D.D.); (L.F.)
| | - Luciano Flor
- Department of Directional Hospital Management, Padua University Hospital, 35128 Padova, Italy; (D.G.B.); (A.C.); (G.C.); (D.D.); (L.F.)
| | - Joseph-Domenico Gabrieli
- Department of Diagnostic Imaging and Interventional Radiology, Neuroradiology, Padua University Hospital, 35128 Padua, Italy; (G.C.); (M.A.); (J.-D.G.)
| | - Marina Munari
- Anesthesia and Intensive Care Unit, Department of Medicine–DIMED, Padua University Hospital, 35128 Padua, Italy; (M.M.); (P.N.)
| | - Paolo Navalesi
- Anesthesia and Intensive Care Unit, Department of Medicine–DIMED, Padua University Hospital, 35128 Padua, Italy; (M.M.); (P.N.)
| | - Alberto Ponzoni
- Radiology Unit, Department of Diagnostic Imaging and Interventional Radiology, Padua University Hospital, 35128 Padua, Italy; (G.D.C.); (A.P.)
| | - Maria Luisa Scapellato
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Preventive Medicine and Risk Assessment, Padua University Hospital, 35128 Padua, Italy;
| | - Ivo Tiberio
- Emergency-Urgency Department, Intensive Care Unit, Padua University Hospital, 35128 Padua, Italy;
| | - Andrea Vianello
- Respiratory Pathophysiology Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padua University Hospital, 35128 Padua, Italy;
| | - Roberto Stramare
- Department of Medicine–DIMED, Institute of Radiology, Padua University Hospital, 35128 Padua, Italy; (C.G.); (R.S.)
| |
Collapse
|
38
|
Cattelan AM, Sasset L, Di Meco E, Cocchio S, Barbaro F, Cavinato S, Gardin S, Carretta G, Donato D, Crisanti A, Trevenzoli M, Baldo V. An Integrated Strategy for the Prevention of SARS-CoV-2 Infection in Healthcare Workers: A Prospective Observational Study. Int J Environ Res Public Health 2020; 17:ijerph17165785. [PMID: 32785110 PMCID: PMC7460144 DOI: 10.3390/ijerph17165785] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 01/02/2023]
Abstract
Background: Since the beginning of SARS-CoV-2 outbreak, a large number of infections have been reported among healthcare workers (HCWs). The aim of this study was to investigate the occurrence of SARS-CoV-2 infection among HCWs involved in the first management of infected patients and to describe the measures adopted to prevent the transmission in the hospital. Methods: This prospective observational study was conducted between February 21 and April 16, 2020, in the Padua University Hospital (north-east Italy). The infection control policy adopted consisted of the following: the creation of the “Advanced Triage” area for the evaluation of SARS-CoV-2 cases, and the implementation of an integrated infection control surveillance system directed to all the healthcare personnel involved in the Advance Triage area. HCWs were regularly tested with nasopharyngeal swabs for SARS-CoV-2; body temperature and suggestive symptoms were evaluated at each duty. Demographic and clinical data of both patients and HCWs were collected and analyzed; HCWs’ personal protective equipment (PPE) consumption was also recorded. The efficiency of the control strategy among HCWs was evaluated identifying symptomatic infection (primary endpoint) and asymptomatic infection (secondary endpoint) with confirmed detection of SARS-CoV-2. Results: 7595 patients were evaluated in the Advanced Triage area: 5.2% resulted positive and 72.4% was symptomatic. The HCW team was composed of 60 members. A total of 361 nasopharyngeal swabs were performed on HCWs. All the swabs resulted negative and none of the HCWs reached the primary or the secondary endpoint. Conclusions: An integrated hospital infection control strategy, consisting of dedicated areas for infected patients, strict measures for PPE use and mass surveillance, is successful to prevent infection among HCWs.
Collapse
Affiliation(s)
- Anna Maria Cattelan
- Infectious Diseases Unit, Department of Medicine, Azienda Ospedale Università di Padova, 35128 Padova, Italy; (L.S.); (E.D.M.); (F.B.); (S.C.); (S.G.); (M.T.)
- Correspondence: ; Tel.: +0039-333-7138916
| | - Lolita Sasset
- Infectious Diseases Unit, Department of Medicine, Azienda Ospedale Università di Padova, 35128 Padova, Italy; (L.S.); (E.D.M.); (F.B.); (S.C.); (S.G.); (M.T.)
| | - Eugenia Di Meco
- Infectious Diseases Unit, Department of Medicine, Azienda Ospedale Università di Padova, 35128 Padova, Italy; (L.S.); (E.D.M.); (F.B.); (S.C.); (S.G.); (M.T.)
| | - Silvia Cocchio
- Department of Cardiac Thoracic Vascular Sciences and Public Health, University of Padua, 35128 Padova, Italy; (S.C.); (V.B.)
| | - Francesco Barbaro
- Infectious Diseases Unit, Department of Medicine, Azienda Ospedale Università di Padova, 35128 Padova, Italy; (L.S.); (E.D.M.); (F.B.); (S.C.); (S.G.); (M.T.)
| | - Silvia Cavinato
- Infectious Diseases Unit, Department of Medicine, Azienda Ospedale Università di Padova, 35128 Padova, Italy; (L.S.); (E.D.M.); (F.B.); (S.C.); (S.G.); (M.T.)
| | - Samuele Gardin
- Infectious Diseases Unit, Department of Medicine, Azienda Ospedale Università di Padova, 35128 Padova, Italy; (L.S.); (E.D.M.); (F.B.); (S.C.); (S.G.); (M.T.)
| | - Giovanni Carretta
- Health Department, Azienda Ospedale Università di Padova, 35128 Padova, Italy; (G.C.); (D.D.)
| | - Daniele Donato
- Health Department, Azienda Ospedale Università di Padova, 35128 Padova, Italy; (G.C.); (D.D.)
| | - Andrea Crisanti
- Clinical Microbiology and Virology Unit, Department of Molecular Medicine, Azienda Ospedale Università di Padova, 35128 Padova, Italy;
- Department of Life Science, Imperial College London, London SW7 2AZ, UK
| | - Marco Trevenzoli
- Infectious Diseases Unit, Department of Medicine, Azienda Ospedale Università di Padova, 35128 Padova, Italy; (L.S.); (E.D.M.); (F.B.); (S.C.); (S.G.); (M.T.)
| | - Vincenzo Baldo
- Department of Cardiac Thoracic Vascular Sciences and Public Health, University of Padua, 35128 Padova, Italy; (S.C.); (V.B.)
| |
Collapse
|
39
|
Lavezzo E, Franchin E, Ciavarella C, Cuomo-Dannenburg G, Barzon L, Del Vecchio C, Rossi L, Manganelli R, Loregian A, Navarin N, Abate D, Sciro M, Merigliano S, De Canale E, Vanuzzo MC, Besutti V, Saluzzo F, Onelia F, Pacenti M, Parisi SG, Carretta G, Donato D, Flor L, Cocchio S, Masi G, Sperduti A, Cattarino L, Salvador R, Nicoletti M, Caldart F, Castelli G, Nieddu E, Labella B, Fava L, Drigo M, Gaythorpe KAM, Brazzale AR, Toppo S, Trevisan M, Baldo V, Donnelly CA, Ferguson NM, Dorigatti I, Crisanti A. Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'. Nature 2020; 584:425-429. [PMID: 32604404 DOI: 10.1038/s41586-020-2488-1] [Citation(s) in RCA: 623] [Impact Index Per Article: 155.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/23/2020] [Indexed: 01/12/2023]
Abstract
On 21 February 2020, a resident of the municipality of Vo', a small town near Padua (Italy), died of pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection1. This was the first coronavirus disease 19 (COVID-19)-related death detected in Italy since the detection of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. Here we collected information on the demography, clinical presentation, hospitalization, contact network and the presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo' at two consecutive time points. From the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI): 2.1-3.3%). From the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI: 0.8-1.8%). Notably, 42.5% (95% CI: 31.5-54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (that is, did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI: 5.9-9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (P = 0.62 and 0.74 for E and RdRp genes, respectively, exact Wilcoxon-Mann-Whitney test). This study sheds light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides insights into its transmission dynamics and the efficacy of the implemented control measures.
Collapse
Affiliation(s)
- Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Nicolò Navarin
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Davide Abate
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | - Francesca Saluzzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Francesco Onelia
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Saverio G Parisi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Silvia Cocchio
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alessandro Sperduti
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Renato Salvador
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | | | | | - Ludovico Fava
- School of Medicine, University of Padova, Padua, Italy
| | - Matteo Drigo
- School of Medicine, University of Padova, Padua, Italy
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | | | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Vincenzo Baldo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
| | | |
Collapse
|
40
|
Lavezzo E, Franchin E, Ciavarella C, Cuomo-Dannenburg G, Barzon L, Del Vecchio C, Rossi L, Manganelli R, Loregian A, Navarin N, Abate D, Sciro M, Merigliano S, De Canale E, Vanuzzo MC, Besutti V, Saluzzo F, Onelia F, Pacenti M, Parisi SG, Carretta G, Donato D, Flor L, Cocchio S, Masi G, Sperduti A, Cattarino L, Salvador R, Nicoletti M, Caldart F, Castelli G, Nieddu E, Labella B, Fava L, Drigo M, Gaythorpe KAM, Brazzale AR, Toppo S, Trevisan M, Baldo V, Donnelly CA, Ferguson NM, Dorigatti I, Crisanti A. Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'. Nature 2020. [PMID: 32604404 DOI: 10.1101/2020.04.17.20053157] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
On 21 February 2020, a resident of the municipality of Vo', a small town near Padua (Italy), died of pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection1. This was the first coronavirus disease 19 (COVID-19)-related death detected in Italy since the detection of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. Here we collected information on the demography, clinical presentation, hospitalization, contact network and the presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo' at two consecutive time points. From the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI): 2.1-3.3%). From the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI: 0.8-1.8%). Notably, 42.5% (95% CI: 31.5-54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (that is, did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI: 5.9-9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (P = 0.62 and 0.74 for E and RdRp genes, respectively, exact Wilcoxon-Mann-Whitney test). This study sheds light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides insights into its transmission dynamics and the efficacy of the implemented control measures.
Collapse
Affiliation(s)
- Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Nicolò Navarin
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Davide Abate
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | - Francesca Saluzzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Francesco Onelia
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Saverio G Parisi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Silvia Cocchio
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alessandro Sperduti
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Renato Salvador
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | | | | | - Ludovico Fava
- School of Medicine, University of Padova, Padua, Italy
| | - Matteo Drigo
- School of Medicine, University of Padova, Padua, Italy
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Vincenzo Baldo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
| |
Collapse
|
41
|
Basso D, Aita A, Navaglia F, Franchin E, Fioretto P, Moz S, Bozzato D, Zambon CF, Martin B, Dal Prà C, Crisanti A, Plebani M. SARS-CoV-2 RNA identification in nasopharyngeal swabs: issues in pre-analytics. Clin Chem Lab Med 2020; 58:1579-1586. [PMID: 32573469 DOI: 10.1515/cclm-2020-0749] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 05/24/2020] [Indexed: 12/20/2022]
Abstract
Objectives The direct identification of SARS-CoV-2 RNA in nasopharyngeal swabs is recommended for diagnosing the novel COVID-19 disease. Pre-analytical determinants, such as sampling procedures, time and temperature storage conditions, might impact on the end result. Our aim was to evaluate the effects of sampling procedures, time and temperature of the primary nasopharyngeal swabs storage on real-time reverse-transcription polymerase chain reaction (rRT-PCR) results. Methods Each nasopharyngeal swab obtained from 10 hospitalized patients for COVID-19 was subdivided in 15 aliquots: five were kept at room temperature; five were refrigerated (+4 °C); five were immediately mixed with the extraction buffer and refrigerated at +4 °C. Every day and for 5 days, one aliquot per condition was analyzed (rRT-PCR) for SARS-CoV-2 gene E and RNaseP and threshold cycles (Ct) compared. To evaluate manual sampling, 70 nasopharyngeal swabs were sampled twice by two different operators and analyzed separately one from the other. Results A total of 6/10 swabs were SARS-CoV-2 positive. No significant time or storage-dependent variations were observed in SARS-CoV-2 Ct. Re-sampling of swabs with SARS-CoV-2 Ct lower than 33 resulted in highly reproducible results (CV=2.9%), while a high variability was observed when Ct values were higher than 33 (CV=10.3%). Conclusions This study demonstrates that time and temperature of nasopharyngeal swabs storage do not significantly impact on results reproducibility. However, swabs sampling is a critical step, and especially in case of low viral load, might be a potential source of diagnostic errors.
Collapse
Affiliation(s)
- Daniela Basso
- Department of Medicine - DIMED, University of Padova, Padova, Italy
- Department of Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Ada Aita
- Department of Medicine - DIMED, University of Padova, Padova, Italy
- Department of Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Filippo Navaglia
- Department of Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Elisa Franchin
- Department of Molecular Medicine - DMM, Microbiology and Virology, University of Padova, Padova, Italy
| | - Paola Fioretto
- Department of Medicine - DIMED, Internal Medicine 3, University of Padova, Padova, Italy
| | - Stefania Moz
- Department of Medicine - DIMED, University of Padova, Padova, Italy
- Department of Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Dania Bozzato
- Department of Medicine - DIMED, University of Padova, Padova, Italy
- Department of Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Carlo-Federico Zambon
- Department of Medicine - DIMED, University of Padova, Padova, Italy
- Department of Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Barbara Martin
- Department of Medicine - DIMED, Internal Medicine 3, University of Padova, Padova, Italy
| | - Chiara Dal Prà
- Department of Medicine - DIMED, Internal Medicine 3, University of Padova, Padova, Italy
| | - Andrea Crisanti
- Department of Molecular Medicine - DMM, Microbiology and Virology, University of Padova, Padova, Italy
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Mario Plebani
- Department of Medicine - DIMED, University of Padova, Padova, Italy
- Department of Laboratory Medicine, University Hospital of Padova, Padova, Italy
| |
Collapse
|
42
|
Basso C, Calabrese F, Sbaraglia M, Del Vecchio C, Carretta G, Saieva A, Donato D, Flor L, Crisanti A, Dei Tos AP. Feasibility of postmortem examination in the era of COVID-19 pandemic: the experience of a Northeast Italy University Hospital. Virchows Arch 2020; 477:341-347. [PMID: 32519035 PMCID: PMC7282199 DOI: 10.1007/s00428-020-02861-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/19/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
With the continuous spreading of SARS-CoV-2 and increasing number of deaths worldwide, the need and appropriateness for autopsy in patients with COVID-19 became a matter of discussion. In fact, in the COVID-19 era protection of healthcare workers is a priority besides patient management. No evidence is currently available about the real risk related to the procedure as well as to the subsequent management of the samples. We herein describe the procedure that has been used to perform the first series of postmortem examinations in the COVID center of the Padua University Hospital, Padua, Italy, after the implementation of an ad hoc operating procedure, to minimize the risk of infection for pathologists and technicians. Provided that the procedure is performed in an adequate environment respecting strict biosafety rules, our data indicate that complete postmortem examination appears to be safe and will be highly informative providing useful insights into the complex disease pathogenesis.
Collapse
Affiliation(s)
- Cristina Basso
- Cardiovascular Pathology Unit, Padua University Hospital, Padua, Italy.
- Department of Cardiac Thoracic and Vascular Sciences and Public Health, University of Padua, Padua, Italy.
| | - Fiorella Calabrese
- Cardiovascular Pathology Unit, Padua University Hospital, Padua, Italy
- Department of Cardiac Thoracic and Vascular Sciences and Public Health, University of Padua, Padua, Italy
| | - Marta Sbaraglia
- Pathology Unit, Padua University Hospital, Padua, Italy
- Department of Medicine, University of Padua, Padua, Italy
| | - Claudia Del Vecchio
- Microbiology and Virology Unit, Padua University Hospital, Padua, Italy
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | | | - Daniele Donato
- Chief Medical Office, Padua University Hospital, Padua, Italy
| | - Luciano Flor
- Chief Medical Office, Padua University Hospital, Padua, Italy
| | - Andrea Crisanti
- Microbiology and Virology Unit, Padua University Hospital, Padua, Italy
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Angelo Paolo Dei Tos
- Pathology Unit, Padua University Hospital, Padua, Italy.
- Department of Medicine, University of Padua, Padua, Italy.
| |
Collapse
|
43
|
Simoni A, Hammond AM, Beaghton AK, Galizi R, Taxiarchi C, Kyrou K, Meacci D, Gribble M, Morselli G, Burt A, Nolan T, Crisanti A. A male-biased sex-distorter gene drive for the human malaria vector Anopheles gambiae. Nat Biotechnol 2020; 38:1054-1060. [PMID: 32393821 PMCID: PMC7473848 DOI: 10.1038/s41587-020-0508-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 04/01/2020] [Indexed: 12/21/2022]
Abstract
Only female insects transmit diseases such as malaria, dengue and Zika; therefore, control methods that bias the sex ratio of insect offspring have long been sought. Genetic elements such as sex-chromosome drives can distort sex ratios to produce unisex populations that eventually collapse, but the underlying molecular mechanisms are unknown. We report a male-biased sex-distorter gene drive (SDGD) in the human malaria vector Anopheles gambiae. We induced super-Mendelian inheritance of the X-chromosome-shredding I-PpoI nuclease by coupling this to a CRISPR-based gene drive inserted into a conserved sequence of the doublesex (dsx) gene. In modeling of invasion dynamics, SDGD was predicted to have a quicker impact on female mosquito populations than previously developed gene drives targeting female fertility. The SDGD at the dsx locus led to a male-only population from a 2.5% starting allelic frequency in 10–14 generations, with population collapse and no selection for resistance. Our results support the use of SDGD for malaria vector control. A sex-distorter gene drive causes population collapse in the malaria mosquito.
Collapse
Affiliation(s)
- Alekos Simoni
- Department of Life Sciences, Imperial College London, London, UK.,Polo d'Innovazione Genomica, Genetica e Biologia, Terni, Italy
| | - Andrew M Hammond
- Department of Life Sciences, Imperial College London, London, UK.,W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA
| | | | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, UK.,Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
| | | | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, London, UK
| | - Dario Meacci
- Department of Life Sciences, Imperial College London, London, UK
| | - Matthew Gribble
- Department of Life Sciences, Imperial College London, London, UK
| | - Giulia Morselli
- Department of Life Sciences, Imperial College London, London, UK
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, UK
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, London, UK.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK. .,Department of Molecular Medicine, University of Padova, Padova, Italy.
| |
Collapse
|
44
|
Seccia R, Gammelli D, Dominici F, Romano S, Landi AC, Salvetti M, Tacchella A, Zaccaria A, Crisanti A, Grassi F, Palagi L. Considering patient clinical history impacts performance of machine learning models in predicting course of multiple sclerosis. PLoS One 2020; 15:e0230219. [PMID: 32196512 PMCID: PMC7083323 DOI: 10.1371/journal.pone.0230219] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/24/2020] [Indexed: 12/27/2022] Open
Abstract
Multiple Sclerosis (MS) progresses at an unpredictable rate, but predictions on the disease course in each patient would be extremely useful to tailor therapy to the individual needs. We explore different machine learning (ML) approaches to predict whether a patient will shift from the initial Relapsing-Remitting (RR) to the Secondary Progressive (SP) form of the disease, using only "real world" data available in clinical routine. The clinical records of 1624 outpatients (207 in the SP phase) attending the MS service of Sant'Andrea hospital, Rome, Italy, were used. Predictions at 180, 360 or 720 days from the last visit were obtained considering either the data of the last available visit (Visit-Oriented setting), comparing four classical ML methods (Random Forest, Support Vector Machine, K-Nearest Neighbours and AdaBoost) or the whole clinical history of each patient (History-Oriented setting), using a Recurrent Neural Network model, specifically designed for historical data. Missing values were handled by removing either all clinical records presenting at least one missing parameter (Feature-saving approach) or the 3 clinical parameters which contained missing values (Record-saving approach). The performances of the classifiers were rated using common indicators, such as Recall (or Sensitivity) and Precision (or Positive predictive value). In the visit-oriented setting, the Record-saving approach yielded Recall values from 70% to 100%, but low Precision (5% to 10%), which however increased to 50% when considering only predictions for which the model returned a probability above a given "confidence threshold". For the History-oriented setting, both indicators increased as prediction time lengthened, reaching values of 67% (Recall) and 42% (Precision) at 720 days. We show how "real world" data can be effectively used to forecast the evolution of MS, leading to high Recall values and propose innovative approaches to improve Precision towards clinically useful values.
Collapse
Affiliation(s)
- Ruggiero Seccia
- Dept. of Computer, Control and Management Engineering Antonio Ruberti, Sapienza University of Rome, Rome, Italy
| | - Daniele Gammelli
- Dept. of Computer, Control and Management Engineering Antonio Ruberti, Sapienza University of Rome, Rome, Italy
| | - Fabio Dominici
- Dept. of Computer, Control and Management Engineering Antonio Ruberti, Sapienza University of Rome, Rome, Italy
| | - Silvia Romano
- Dept. of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy
| | - Anna Chiara Landi
- Dept. of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy
| | - Marco Salvetti
- Dept. of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy
- IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Italy
| | - Andrea Tacchella
- Dept. of Physics, Istituto dei Sistemi Complessi (ISC)-CNR, UOS Sapienza, Rome, Italy
| | - Andrea Zaccaria
- Dept. of Physics, Istituto dei Sistemi Complessi (ISC)-CNR, UOS Sapienza, Rome, Italy
| | | | - Francesca Grassi
- Dept. of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Laura Palagi
- Dept. of Computer, Control and Management Engineering Antonio Ruberti, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
45
|
Abstract
Gene drive is a natural process of biased inheritance that, in principle, could be used to control pest and vector populations. As with any form of pest control, attention should be paid to the possibility of resistance evolving. For nuclease-based gene drive aimed at suppressing a population, resistance could arise by changes in the target sequence that maintain function, and various strategies have been proposed to reduce the likelihood that such alleles arise. Even if these strategies are successful, it is almost inevitable that alleles will arise at the target site that are resistant to the drive but do not restore function, and the impact of such sequences on the dynamics of control has been little studied. We use population genetic modelling of a strategy targeting a female fertility gene to demonstrate that such alleles may be expected to accumulate, and thereby reduce the reproductive load on the population, if nuclease expression per se causes substantial heterozygote fitness effects or if parental (especially paternal) deposition of nuclease either reduces offspring fitness or affects the genotype of their germline. All these phenomena have been observed in synthetic drive constructs. It will, therefore, be important to allow for non-functional resistance alleles in predicting the dynamics of constructs in cage populations and the impacts of any field release.
Collapse
Affiliation(s)
- Andrea K Beaghton
- Department of Life Sciences, Imperial College, South Kensington, London SW7 2AZ, UK
| | - Andrew Hammond
- Department of Life Sciences, Imperial College, South Kensington, London SW7 2AZ, UK
| | - Tony Nolan
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College, South Kensington, London SW7 2AZ, UK
| | - Austin Burt
- Department of Life Sciences, Imperial College, Silwood Park, Ascot, Berkshire SL5 7PY, UK
| |
Collapse
|
46
|
Bernardini F, Kriezis A, Galizi R, Nolan T, Crisanti A. Introgression of a synthetic sex ratio distortion system from Anopheles gambiae into Anopheles arabiensis. Sci Rep 2019; 9:5158. [PMID: 30914785 PMCID: PMC6435806 DOI: 10.1038/s41598-019-41646-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/14/2019] [Indexed: 12/04/2022] Open
Abstract
I-PpoI is a homing endonuclease that has a high cleavage activity and specificity for a conserved sequence within the ribosomal rDNA repeats, located in a single cluster on the Anopheles gambiae X chromosome. This property has been exploited to develop a synthetic sex ratio distortion system in this mosquito species. When I-PpoI is expressed from a transgene during spermatogenesis in mosquitoes, the paternal X chromosome is shredded and only Y chromosome-bearing sperm are viable, resulting in a male-biased sex ratio of >95% in the progeny. These distorter male mosquitoes can efficiently suppress caged wild-type populations, providing a powerful tool for vector control strategies. Given that malaria mosquito vectors belong to a species complex comprising at least two major vectors, we investigated whether the sex distorter I-PpoI, originally integrated in the A. gambiae genome, could be transferred via introgression to the sibling vector species Anopheles arabiensis. In compliance with Haldane’s rule, F1 hybrid male sterility is known to occur in all intercrosses among members of the Anopheles gambiae complex. A scheme based on genetic crosses and transgene selection was used to bypass F1 hybrid male sterility and introgress the sex distorter I-PpoI into the A. arabiensis genetic background. Our data suggest that this sex distortion technique can be successfully applied to target A. arabiensis mosquitoes.
Collapse
Affiliation(s)
- Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Antonios Kriezis
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
| |
Collapse
|
47
|
Facchinelli L, North AR, Collins CM, Menichelli M, Persampieri T, Bucci A, Spaccapelo R, Crisanti A, Benedict MQ. Large-cage assessment of a transgenic sex-ratio distortion strain on populations of an African malaria vector. Parasit Vectors 2019; 12:70. [PMID: 30728060 PMCID: PMC6366042 DOI: 10.1186/s13071-019-3289-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 01/03/2019] [Indexed: 12/25/2022] Open
Abstract
Background Novel transgenic mosquito control methods require progressively more realistic evaluation. The goal of this study was to determine the effect of a transgene that causes a male-bias sex ratio on Anopheles gambiae target populations in large insectary cages. Methods Life history characteristics of Anopheles gambiae wild type and Ag(PMB)1 (aka gfp124L-2) transgenic mosquitoes, whose progeny are 95% male, were measured in order to parameterize predictive population models. Ag(PMB)1 males were then introduced at two ratios into large insectary cages containing target wild type populations with stable age distributions and densities. The predicted proportion of females and those observed in the large cages were compared. A related model was then used to predict effects of male releases on wild mosquitoes in a west African village. Results The frequency of transgenic mosquitoes in target populations reached an average of 0.44 ± 0.02 and 0.56 ± 0.02 after 6 weeks in the 1:1 and in the 3:1 release ratio treatments (transgenic male:wild male) respectively. Transgenic males caused sex-ratio distortion of 73% and 80% males in the 1:1 and 3:1 treatments, respectively. The number of eggs laid in the transgenic treatments declined as the experiment progressed, with a steeper decline in the 3:1 than in the 1:1 releases. The results of the experiment are partially consistent with predictions of the model; effect size and variability did not conform to the model in two out of three trials, effect size was over-estimated by the model and variability was greater than anticipated, possibly because of sampling effects in restocking. The model estimating the effects of hypothetical releases on the mosquito population of a West African village demonstrated that releases could significantly reduce the number of females in the wild population. The interval of releases is not expected to have a strong effect. Conclusions The biological data produced to parameterize the model, the model itself, and the results of the experiments are components of a system to evaluate and predict the performance of transgenic mosquitoes. Together these suggest that the Ag(PMB)1 strain has the potential to be useful for reversible population suppression while this novel field develops.
Collapse
Affiliation(s)
- Luca Facchinelli
- Department of Experimental Medicine, University of Perugia, Perugia, Italy.,Present address: Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Ace R North
- Department of Zoology, University of Oxford, New Radcliffe House, Woodstock Road, Oxford, OX2 6GG, UK
| | - C Matilda Collins
- Centre for Environmental Policy, Imperial College London, 16-18 Princes Gardens, London, SW7 1NE, UK
| | - Miriam Menichelli
- Polo di Genomica Genetica e Biologia, Via mazzieri 3, 05100, Terni, Italy
| | - Tania Persampieri
- Polo di Genomica Genetica e Biologia, Via mazzieri 3, 05100, Terni, Italy
| | - Alessandro Bucci
- Polo di Genomica Genetica e Biologia, Via mazzieri 3, 05100, Terni, Italy
| | - Roberta Spaccapelo
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building Imperial College Road South Kensington, London, SW7 2AZ, UK
| | - Mark Q Benedict
- Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA, 30329, USA.
| |
Collapse
|
48
|
Kyrou K, Hammond AM, Galizi R, Kranjc N, Burt A, Beaghton AK, Nolan T, Crisanti A. A CRISPR-Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes. Nat Biotechnol 2018; 36:1062-1066. [PMID: 30247490 PMCID: PMC6871539 DOI: 10.1038/nbt.4245] [Citation(s) in RCA: 441] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/03/2018] [Indexed: 01/13/2023]
Abstract
Complete population collapse of malaria vector Anopheles gambiae in cages is achieved using a gene drive that targets doublesex. In the human malaria vector Anopheles gambiae, the gene doublesex (Agdsx) encodes two alternatively spliced transcripts, dsx-female (AgdsxF) and dsx-male (AgdsxM), that control differentiation of the two sexes. The female transcript, unlike the male, contains an exon (exon 5) whose sequence is highly conserved in all Anopheles mosquitoes so far analyzed. We found that CRISPR–Cas9-targeted disruption of the intron 4–exon 5 boundary aimed at blocking the formation of functional AgdsxF did not affect male development or fertility, whereas females homozygous for the disrupted allele showed an intersex phenotype and complete sterility. A CRISPR–Cas9 gene drive construct targeting this same sequence spread rapidly in caged mosquitoes, reaching 100% prevalence within 7–11 generations while progressively reducing egg production to the point of total population collapse. Owing to functional constraint of the target sequence, no selection of alleles resistant to the gene drive occurred in these laboratory experiments. Cas9-resistant variants arose in each generation at the target site but did not block the spread of the drive.
Collapse
Affiliation(s)
- Kyros Kyrou
- Department of Life Sciences, Imperial College London, UK
| | | | - Roberto Galizi
- Department of Life Sciences, Imperial College London, UK
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, UK
| | - Austin Burt
- Department of Life Sciences, Imperial College London, UK
| | | | - Tony Nolan
- Department of Life Sciences, Imperial College London, UK
| | | |
Collapse
|
49
|
Crisanti A, Picco M, Ritort F. Derivation of the spin-glass order parameter from stochastic thermodynamics. Phys Rev E 2018; 97:052103. [PMID: 29906861 DOI: 10.1103/physreve.97.052103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Indexed: 06/08/2023]
Abstract
A fluctuation relation is derived to extract the order parameter function q(x) in weakly ergodic systems. The relation is based on measuring and classifying entropy production fluctuations according to the value of the overlap q between configurations. For a fixed value of q, entropy production fluctuations are Gaussian distributed allowing us to derive the quasi-FDT so characteristic of aging systems. The theory is validated by extracting the q(x) in various types of glassy models. It might be generally applicable to other nonequilibrium systems and experimental small systems.
Collapse
Affiliation(s)
- A Crisanti
- Dipartimento di Fisica, Università di Roma "La Sapienza", and Istituto dei Sistemi Complessi ISC-CNR, P.le Aldo Moro 2, 00185 Roma, Italy
| | - M Picco
- Sorbonne Université, CNRS, Université Pierre et Marie Curie, LPTHE, F-75005 Paris, France
| | - F Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, C/ Martí i Franquès, E-08028, Barcelona, Spain
- CIBER-BBN Center for Bioengineering, Biomaterials and Nanomedicine, Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
50
|
Burt A, Crisanti A. Editorial: gene drive for vector control. Pathog Glob Health 2018; 111:397-398. [PMID: 29561232 DOI: 10.1080/20477724.2018.1453581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Austin Burt
- a Faculty of Natural Sciences, Department of Life Sciences , Imperial College London
| | - Andrea Crisanti
- a Faculty of Natural Sciences, Department of Life Sciences , Imperial College London
| |
Collapse
|