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5 results on '"Delaunay-Moisan, Agnès"'

1. Screening for SARS-CoV-2 by RT-PCR: Saliva or nasopharyngeal swab? Rapid review and meta-analysis.

Author

Ibrahimi N, Delaunay-Moisan A, Hill C, Le Teuff G, Rupprecht JF, Thuret JY, Chaltiel D, and Potier MC

Subjects
Humans, RNA, Viral genetics, SARS-CoV-2 genetics, Sensitivity and Specificity, Specimen Handling methods, COVID-19 diagnosis, COVID-19 Nucleic Acid Testing methods, Nasopharynx virology, RNA, Viral analysis, SARS-CoV-2 isolation & purification, Saliva virology
Abstract

Background: Diagnosis of COVID-19 in symptomatic patients and screening of populations for SARS-CoV-2 infection require access to straightforward, low-cost and high-throughput testing. The recommended nasopharyngeal swab tests are limited by the need of trained professionals and specific consumables and this procedure is poorly accepted as a screening method In contrast, saliva sampling can be self-administered., Methods: In order to compare saliva and nasopharyngeal/oropharyngeal samples for the detection of SARS-CoV-2, we designed a meta-analysis searching in PubMed up to December 29th, 2020 with the key words "(SARS-CoV-2 OR COVID-19 OR COVID19) AND (salivary OR saliva OR oral fluid)) NOT (review[Publication Type]) NOT (PrePrint[Publication Type])" applying the following criteria: records published in peer reviewed scientific journals, in English, with at least 15 nasopharyngeal/orapharyngeal swabs and saliva paired samples tested by RT-PCR, studies with available raw data including numbers of positive and negative tests with the two sampling methods. For all studies, concordance and sensitivity were calculated and then pooled in a random-effects model., Findings: A total of 377 studies were retrieved, of which 50 were eligible, reporting on 16,473 pairs of nasopharyngeal/oropharyngeal and saliva samples. Meta-analysis showed high concordance, 92.5% (95%CI: 89.5-94.7), across studies and pooled sensitivities of 86.5% (95%CI: 83.4-89.1) and 92.0% (95%CI: 89.1-94.2) from saliva and nasopharyngeal/oropharyngeal swabs respectively. Heterogeneity across studies was 72.0% for saliva and 85.0% for nasopharyngeal/oropharyngeal swabs., Interpretation: Our meta-analysis strongly suggests that saliva could be used for frequent testing of COVID-19 patients and "en masse" screening of populations., Competing Interests: The authors have declared that no competing interests exist.

Published
2021
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2. SARS-CoV-2 biology and variants: anticipation of viral evolution and what needs to be done.

Author

Luo R, Delaunay-Moisan A, Timmis K, and Danchin A

Subjects
COVID-19 epidemiology, COVID-19 genetics, Disease Transmission, Infectious prevention & control, Genetic Variation, Host-Pathogen Interactions, Humans, SARS-CoV-2 physiology, Virus Replication, Biological Evolution, COVID-19 prevention & control, COVID-19 virology, SARS-CoV-2 genetics
Abstract

The global propagation of SARS-CoV-2 and the detection of a large number of variants, some of which have replaced the original clade to become dominant, underscores the fact that the virus is actively exploring its evolutionary space. The longer high levels of viral multiplication occur - permitted by high levels of transmission -, the more the virus can adapt to the human host and find ways to success. The third wave of the COVID-19 pandemic is starting in different parts of the world, emphasizing that transmission containment measures that are being imposed are not adequate. Part of the consideration in determining containment measures is the rationale that vaccination will soon stop transmission and allow a return to normality. However, vaccines themselves represent a selection pressure for evolution of vaccine-resistant variants, so the coupling of a policy of permitting high levels of transmission/virus multiplication during vaccine roll-out with the expectation that vaccines will deal with the pandemic, is unrealistic. In the absence of effective antivirals, it is not improbable that SARS-CoV-2 infection prophylaxis will involve an annual vaccination campaign against 'dominant' viral variants, similar to influenza prophylaxis. Living with COVID-19 will be an issue of SARS-CoV-2 variants and evolution. It is therefore crucial to understand how SARS-CoV-2 evolves and what constrains its evolution, in order to anticipate the variants that will emerge. Thus far, the focus has been on the receptor-binding spike protein, but the virus is complex, encoding 26 proteins which interact with a large number of host factors, so the possibilities for evolution are manifold and not predictable a priori. However, if we are to mount the best defence against COVID-19, we must mount it against the variants, and to do this, we must have knowledge about the evolutionary possibilities of the virus. In addition to the generic cellular interactions of the virus, there are extensive polymorphisms in humans (e.g. Lewis, HLA, etc.), some distributed within most or all populations, some restricted to specific ethnic populations and these variations pose additional opportunities for/constraints on viral evolution. We now have the wherewithal - viral genome sequencing, protein structure determination/modelling, protein interaction analysis - to functionally characterize viral variants, but access to comprehensive genome data is extremely uneven. Yet, to develop an understanding of the impacts of such evolution on transmission and disease, we must link it to transmission (viral epidemiology) and disease data (patient clinical data), and the population granularities of these. In this editorial, we explore key facets of viral biology and the influence of relevant aspects of human polymorphisms, human behaviour, geography and climate and, based on this, derive a series of recommendations to monitor viral evolution and predict the types of variants that are likely to arise., (© 2021 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Published
2021
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3. Prior infection by seasonal coronaviruses, as assessed by serology, does not prevent SARS-CoV-2 infection and disease in children, France, April to June 2020.

Author

Sermet-Gaudelus I, Temmam S, Huon C, Behillil S, Gajdos V, Bigot T, Lurier T, Chrétien D, Backovic M, Delaunay-Moisan A, Donati F, Albert M, Foucaud E, Mesplées B, Benoist G, Faye A, Duval-Arnould M, Cretolle C, Charbit M, Aubart M, Auriau J, Lorrot M, Kariyawasam D, Fertitta L, Orliaguet G, Pigneur B, Bader-Meunier B, Briand C, Enouf V, Toubiana J, Guilleminot T, van der Werf S, Leruez-Ville M, and Eloit M

Subjects
Adolescent, Antibodies, Viral blood, COVID-19 blood, COVID-19 diagnosis, Child, Child, Preschool, Cross-Sectional Studies, Female, France epidemiology, Humans, Infant, Infant, Newborn, Male, Paris, Seasons, Serologic Tests methods, Spike Glycoprotein, Coronavirus, Antibodies, Viral immunology, COVID-19 immunology, Coronavirus OC43, Human, SARS-CoV-2 immunology, Systemic Inflammatory Response Syndrome
Abstract

BackgroundChildren have a low rate of COVID-19 and secondary severe multisystem inflammatory syndrome (MIS) but present a high prevalence of symptomatic seasonal coronavirus infections.AimWe tested if prior infections by seasonal coronaviruses (HCoV) NL63, HKU1, 229E or OC43 as assessed by serology, provide cross-protective immunity against SARS-CoV-2 infection.MethodsWe set a cross-sectional observational multicentric study in pauci- or asymptomatic children hospitalised in Paris during the first wave for reasons other than COVID (hospitalised children (HOS), n = 739) plus children presenting with MIS (n = 36). SARS-CoV-2 antibodies directed against the nucleoprotein (N) and S1 and S2 domains of the spike (S) proteins were monitored by an in-house luciferase immunoprecipitation system assay. We randomly selected 69 SARS-CoV-2-seropositive patients (including 15 with MIS) and 115 matched SARS-CoV-2-seronegative patients (controls (CTL)). We measured antibodies against SARS-CoV-2 and HCoV as evidence for prior corresponding infections and assessed if SARS-CoV-2 prevalence of infection and levels of antibody responses were shaped by prior seasonal coronavirus infections.ResultsPrevalence of HCoV infections were similar in HOS, MIS and CTL groups. Antibody levels against HCoV were not significantly different in the three groups and were not related to the level of SARS-CoV-2 antibodies in the HOS and MIS groups. SARS-CoV-2 antibody profiles were different between HOS and MIS children.ConclusionPrior infection by seasonal coronaviruses, as assessed by serology, does not interfere with SARS-CoV-2 infection and related MIS in children.

Published
2021
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4. The importance of naturally attenuated SARS‐CoV ‐2 in the fight against COVID ‐19

Author

Armengaud, Jean, Delaunay‐Moisan, Agnès, Thuret, Jean‐Yves, Anken, Eelco, Acosta‐Alvear, Diego, Aragón, Tomás, Arias, Carolina, Blondel, Marc, Braakman, Ineke, Collet, Jean‐François, Courcol, René, Danchin, Antoine, Deleuze, Jean‐François, Lavigne, Jean‐Philippe, Lucas, Sophie, Michiels, Thomas, Moore, Edward R. B., Nixon‐Abell, Jonathon, Rossello‐Mora, Ramon, Shi, Zheng‐Li, Siccardi, Antonio G., Sitia, Roberto, Tillett, Daniel, Timmis, Kenneth N., Toledano, Michel B., Sluijs, Peter, Vicenzi, Elisa, Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Stress Oxydatif et Cancer (SOC), Département Biologie Cellulaire (BioCell), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Sénescence et stabilité génomique (SEN), Département Biologie des Génomes (DBG), San Raffaele Scientific Institute, Vita-Salute San Raffaele University and Center for Translational Genomics and Bioinformatics, University of California [Santa Barbara] (UC Santa Barbara), University of California (UC), Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA), Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), EFS-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Université de Bretagne Occidentale - UFR Médecine et Sciences de la Santé (UBO UFR MSS), Utrecht University [Utrecht], Université Catholique de Louvain = Catholic University of Louvain (UCL), Walloon Excellence in Life sciences and BIOtechnology [Liège] (WELBIO), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Virulence bactérienne et maladies infectieuses (VBMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), University of Gothenburg (GU), Sahlgrenska University Hospital [Gothenburg], University of Cambridge [UK] (CAM), Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de las Islas Baleares (UIB), Wuhan Institute of Virology [Wuhan, China], Chinese Academy of Sciences [Wuhan Branch], Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], ANR-17-CE18-0023,Phylopeptidomics,Identification rapide de bactéries pathogènes et résistances aux antibiotiques(2017), Armengaud, Jean [0000-0003-1589-445X], Thuret, Jean-Yves [0000-0001-5385-7620], Anken, Eelco van [0000-0001-9529-2701], Acosta-Alvear, Diego [0000-0002-1139-8486], Aragón, Tomás [0000-0002-1700-2729], Arias, Carolina [0000-0002-4445-0826], Blondel, Marc [0000-0003-4897-2995], Braakman, Ineke [0000-0003-1592-4364], Collet, Jean-François [0000-0001-8069-7036], Courcol, René [0000-0003-2324-5687], Danchin, Antoine [0000-0002-6350-5001], Deleuze, Jean-François [0000-0002-5358-4463], Lavigne, Jean-Philippe [0000-0002-9484-0304], Lucas, Sophie [0000-0003-1287-7996], Michiels, Thomas [0000-0001-9615-8053], Moore, Edward R.B. [0000-0001-7693-924X], Nixon-Abell, Jonathon [0000-0003-4169-0012], Rosselló-Mora, Ramón [0000-0001-8253-3107], Shi, Zheng-Li [0000-0001-8089-163X], Siccardi, Antonio G. [0000-0002-1654-5545], Sitia, Roberto [0000-0001-7086-4152], Tillett, Daniel [0000-0003-1061-0489], Timmis, Kenneth N. [0000-0002-0066-4670], Toledano, Michel B. [0000-0002-3079-1179], Sluijs, Peter van der [0000-0002-4485-3342], Vicenzi, Elisa [0000-0003-0051-3968], University of California [Santa Barbara] (UCSB), University of California, Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Technical University Braunschweig, Armengaud, Jean, Thuret, Jean-Yves, Anken, Eelco van, Acosta-Alvear, Diego, Aragón, Tomás, Arias, Carolina, Blondel, Marc, Braakman, Ineke, Collet, Jean-François, Courcol, René, Danchin, Antoine, Deleuze, Jean-François, Lavigne, Jean-Philippe, Lucas, Sophie, Michiels, Thomas, Moore, Edward R.B., Nixon-Abell, Jonathon, Rosselló-Mora, Ramón, Shi, Zheng-Li, Siccardi, Antonio G., Sitia, Roberto, Tillett, Daniel, Timmis, Kenneth N., Toledano, Michel B., Sluijs, Peter van der, Vicenzi, Elisa, Armengaud, J., Delaunay-Moisan, A., Thuret, J. -Y., van Anken, E., Acosta-Alvear, D., Aragon, T., Arias, C., Blondel, M., Braakman, I., Collet, J. -F., Courcol, R., Danchin, A., Deleuze, J. -F., Lavigne, J. -P., Lucas, S., Michiels, T., Moore, E. R. B., Nixon-Abell, J., Rossello-Mora, R., Shi, Z., Siccardi, A. G., Sitia, R., Tillett, D., Timmis, K. N., Toledano, M. B., van der Sluijs, P., Vicenzi, E., and UCL - SSS/DDUV - Institut de Duve

Subjects
Opinion, viruses, Pneumonia, Viral, Gene Expression, Microbiology, Disease Outbreaks, Evolution, Molecular, Betacoronavirus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Animals, Humans, Health emergency, Selection, Genetic, Pandemics, Ecology, Evolution, Behavior and Systematics, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Virulence, SARS-CoV-2, fungi, COVID-19, SARS Virus, Adaptation, Physiological, Severe acute respiratory syndrome-related coronavirus, Host-Pathogen Interactions, Mutation, Spike Glycoprotein, Coronavirus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Coronavirus Infections
Abstract

The current SARS‐CoV‐2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID‐19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS‐CoV‐2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS‐CoV‐2 would offer significant relief, although vaccine developers have warned that design, testing and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (i), but the earliest vaccines were based on the live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS‐CoV‐2 will mutate and may naturally attenuate over time (ii). What makes the current pandemic unique is that, thanks to state‐of‐the‐art nucleic acid sequencing technologies, we can follow in detail how SARS‐CoV‐2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS‐CoV‐2 variants across the globe should be of key interest in our fight against the pandemic.

Published
2020
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5. The importance of naturally attenuated SARS‐CoV‐2in the fight against COVID‐19.

Author

Armengaud, Jean, Delaunay‐Moisan, Agnès, Thuret, Jean‐Yves, Anken, Eelco, Acosta‐Alvear, Diego, Aragón, Tomás, Arias, Carolina, Blondel, Marc, Braakman, Ineke, Collet, Jean‐François, Courcol, René, Danchin, Antoine, Deleuze, Jean‐François, Lavigne, Jean‐Philippe, Lucas, Sophie, Michiels, Thomas, Moore, Edward R. B., Nixon‐Abell, Jonathon, Rossello‐Mora, Ramon, and Shi, Zheng‐Li

Subjects
COVID-19, PANDEMICS, SARS-CoV-2, ANTIVIRUS software, NUCLEIC acids, VACCINE trials, WORLD health
Abstract

The current SARS‐CoV‐2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID‐19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS‐CoV‐2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS‐CoV‐2 would offer significant relief, although vaccine developers have warned that design, testing and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (i), but the earliest vaccines were based on the live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS‐CoV‐2 will mutate and may naturally attenuate over time (ii). What makes the current pandemic unique is that, thanks to state‐of‐the‐art nucleic acid sequencing technologies, we can follow in detail how SARS‐CoV‐2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS‐CoV‐2 variants across the globe should be of key interest in our fight against the pandemic. [ABSTRACT FROM AUTHOR]

Published
2020
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