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description Publicationkeyboard_double_arrow_right Article , Preprint 2022 FrancePublisher:Cold Spring Harbor Laboratory Funded by:NIH | Inter-regional study of t..., EC | EVA-GLOBAL, ANR | INCEPTION +2 projectsNIH| Inter-regional study of transmission, adaptation and pathogenesis of viruses with pandemic potential in Southeast Asia and West/Central Africa ,EC| EVA-GLOBAL ,ANR| INCEPTION ,EC| RECoVER ,EC| EVAgFranck Touret; Emilie Giraud; Jérôme Bourret; Flora Donati; Jaouen Tran-Rajau; Jeanne Chiaravalli; Frédéric Lemoine; Fabrice Agou; Etienne Simon-Lorière; Sylvie van der Werf; Xavier de Lamballerie;SummaryThe landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple sub-variants originating from BA.2, BA.4 and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1 and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1 and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1 and XBB variants.
iScience arrow_drop_down HAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-IRDArticle . 2023License: CC BY NC NDadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess Routesgold 15 citations 15 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!more_vert iScience arrow_drop_down HAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-IRDArticle . 2023License: CC BY NC NDadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publication2022 France EnglishPublisher:HAL CCSD Funded by:EC | VEO, ANR | INCEPTION, EC | RECoVER +1 projectsEC| VEO ,ANR| INCEPTION ,EC| RECoVER ,ANR| TheraCoVAuthors: Layan, Maylis;Layan, Maylis;Parmi les méthodes pour l'étude quantitative de la transmission des maladies infectieuses dans les populations, les épidémiologistes ont récemment focalisé leur attention sur l'épidémiologie moléculaire qui vise à reconstruire la phylogénie des pathogènes en utilisant leurs séquences génétiques, et la modélisation mathématique des maladies infectieuses qui ajuste des modèles mécanistes de transmission des maladies à des données épidémiologiques telles que le nombre de cas. Ces deux approches se basent sur des données très différentes dont la disponibilité varie selon le contexte. Les concepts et les modèles qu'elles utilisent permettent d'explorer des facettes différentes de la transmission des maladies. L'objectif principal de cette thèse est de mieux comprendre comment les maladies virales comme la rage et la covid-19 circulent dans les populations hôtes en utilisant pour la première des séquences génétiques virales datées et géolocalisées, et pour la deuxième, des données épidémiologiques à l'échelle individuelle. La première partie de cette thèse s'intéresse à la rage, une zoonose tropicale négligée, responsable d'environ 59,000 morts chaque année principalement dans les populations pauvres et rurales d'Afrique et d'Asie. Son agent étiologique, le virus de la rage (RABV), circule principalement dans les populations canines domestiques dont les modes de transmission restent peu étudiés et mal compris malgré l'existence de vaccins efficaces chez l'homme et l'animal. Nous avons tout d'abord synthétisé dans une revue de la littérature l'apport relatif des modèles mathématiques et de l'épidémiologie moléculaire dans la compréhension des dynamiques de la rage chez le chien. Puis, nous avons décrit la circulation endémique de la rage au Cambodge, un des pays les plus affectés, à partir de génomes de la rage isolés chez le chien et analysés avec des méthodes de phylogéographie Bayésienne continue. Nous avons montré que les introductions depuis d'autres pays ne sont pas nécessaires au maintien de la circulation. Toutefois, ces résultats sont conditionnés par l'échantillonnage des génomes. Pour mieux comprendre leurs impacts sur les méthodes de phylogéographie Bayésienne, nous avons entrepris une étude de simulation dans laquelle nous avons comparé les performances de trois algorithmes de phylogéographie discrète face à un échantillonnage plus ou moins biaisé. Nous avons testé des stratégies d'échantillonnage alternatives et intégré des données épidémiologiques afin d'atténuer l'effet potentiel des biais d'échantillonnage sur la performance des trois algorithmes. La deuxième partie de la thèse se concentre sur la transmission du SARS-CoV-2 dans une des plus petites populations, les ménages. Cette configuration est particulièrement adaptée au suivi détaillé de l'ensemble des membres du foyer après l'introduction d'un cas et permet ainsi d'évaluer comment la susceptibilité et l'infectivité varient au niveau individuel. Dans un premier temps, nous avons estimé l'effectivité vaccinale contre l'infection et la transmission si infecté pendant la vague de variant Alpha en Israël grâce à un modèle de transmission dans des ménages partiellement vaccinés. Nous avons ensuite exploré comment l'hétérogénéité de contact dans les ménages, notamment entre les adultes et les enfants, impacte les estimations de l'infectivité et de la susceptibilité relatives des enfants par rapport aux adultes. En conclusion, cette thèse explore les contributions de l'épidémiologie moléculaire et de la modélisation pour la compréhension de la transmission des maladies infectieuses à différentes échelles de population et souligne la nécessité d'intégrer les données génétiques et épidémiologiques. Among the methods for the quantitative study of infectious diseases transmission in host populations, molecular epidemiology that reconstructs pathogen phylogenies by using pathogen genetic sequences and mathematical modelling of infectious diseases that fits mechanistic models of disease transmission to epidemiological data such as case counts are of particular interest to epidemiologists. These two approaches rely on different data sources whose availability depends on the setting. They also rely on different concepts and models leading to complementary pictures of disease transmission. The main objective of this thesis is to better understand how viral infectious diseases such as rabies and COVID-19 circulate in host populations using respectively geolocated and timestamped viral genetic sequences and detailed epidemiological data at the individual level. The first part of this thesis focuses on rabies, a neglected tropical zoonosis, that is estimated to cause 59,000 human deaths per year mostly among rural and poor populations in Africa and Asia. Its causing agent, rabies virus (RABV), mainly circulates in domestic dog populations. Despite being a vaccine-preventable disease in both humans and dogs, rabies remains poorly studied and its circulation in dogs poorly understood. First, we reviewed from the literature all mathematical models and molecular epidemiology studies on dog rabies circulation to synthesize the contribution of both approaches to the understanding of rabies dynamics in dogs. Then, we described RABV spread in Cambodia, one of the most affected countries worldwide, using RABV genomes isolated from dogs and Bayesian continuous phylogeography methods. We used Cambodia as a model of endemic circulation of RABV and exemplified how phylogeography can help characterize circulation in such context. We found that introductions from foreign countries are not necessary to sustain transmission in Cambodia. However, these results are conditional on the sampling of the RABV genomes. To further understand how sampling affects Bayesian phylogeography methods, we performed a simulation study where we evaluated the performances of three Bayesian discrete phylogeography algorithms under increasing levels of bias, and tested whether alternative sampling strategies, and integration of incidence data improve the performances of the algorithms under biased sampling conditions. The second part of this thesis concentrates on SARS-CoV-2 transmission at one of the smallest population scale, households. This setting is particularly suitable to detailed follow-up of household members after introduction of a case, and thus, enables to evaluate how susceptibility and infectivity vary between individuals. First, we estimated BNT162b2 vaccine effectiveness against infection and against transmission if infected during the Alpha wave in Israel using a mathematical model of SARS-CoV-2 transmission in partially vaccinated households. We further explored how model misspecification in a context of differing contact patterns between adults and children would impact estimates of relative infectivity and susceptibility of children compared to adults. Overall, this thesis explores how molecular epidemiology and modelling contribute to the understanding of infectious diseases transmission at the population level and highlights the need for data integration.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert HAL-Pasteur arrow_drop_down All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=dedup_wf_002::e81215a3f9f0bb1ca02005b18fc5fa00&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2022 Belgium, France, SpainPublisher:Cold Spring Harbor Laboratory Funded by:NIH | Inter-regional study of t..., ANR | INCEPTION, EC | EVAg +1 projectsNIH| Inter-regional study of transmission, adaptation and pathogenesis of viruses with pandemic potential in Southeast Asia and West/Central Africa ,ANR| INCEPTION ,EC| EVAg ,EC| EVADERAuthors: Delphine Planas; Timothée Bruel; Isabelle Staropoli; Florence Guivel-Benhassine; +21 AuthorsDelphine Planas; Timothée Bruel; Isabelle Staropoli; Florence Guivel-Benhassine; Françoise Porrot; Piet Maes; Ludivine Grzelak; Matthieu Prot; Said Mougari; Cyril Planchais; Julien Puech; Madelina Saliba; Riwan Sahraoui; Florent Fémy; Nathalie Morel; Jérémy Dufloo; Rafael Sanjuán; Hugo Mouquet; Emmanuel André; Laurent Hocqueloux; Etienne Simon-Loriere; David Veyer; Thierry Prazuck; Hélène Péré; Olivier Schwartz;handle: 10261/283495
pmc: PMC9681044 , PMC9926440
Convergent evolution of SARS-CoV-2 Omicron BA.2, BA.4 and BA.5 lineages has led to the emergence of several new subvariants, including BA.2.75.2, BA.4.6. and BQ.1.1. The subvariants BA.2.75.2 and BQ.1.1 are expected to become predominant in many countries in November 2022. They carry an additional and often redundant set of mutations in the spike, likely responsible for increased transmissibility and immune evasion. Here, we established a viral amplification procedure to easily isolate Omicron strains. We examined their sensitivity to 6 therapeutic monoclonal antibodies (mAbs) and to 72 sera from Pfizer BNT162b2-vaccinated individuals, with or without BA.1/BA.2 or BA.5 breakthrough infection. Ronapreve (Casirivimab and Imdevimab) and Evusheld (Cilgavimab and Tixagevimab) lost any antiviral efficacy against BA.2.75.2 and BQ.1.1, whereas Xevudy (Sotrovimab) remained weakly active. BQ.1.1 was also resistant to Bebtelovimab. Neutralizing titers in triply vaccinated individuals were low to undetectable against BQ.1.1 and BA.2.75.2, 4 months after boosting. A BA.1/BA.2 breakthrough infection increased these titers, which remained about 18-fold lower against BA.2.75.2 and BQ.1.1, than against BA.1. Reciprocally, a BA.5 breakthrough infection increased more efficiently neutralization against BA.5 and BQ.1.1 than against BA.2.75.2. Thus, the evolution trajectory of novel Omicron subvariants facilitated their spread in immunized populations and raises concerns about the efficacy of most currently available mAbs. No
Nature Communication... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICPreprint . 2022HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEAArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/2022.11.17.516888&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 101 citations 101 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 36visibility views 36 download downloads 115 Powered bymore_vert Nature Communication... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICPreprint . 2022HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEAArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/2022.11.17.516888&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint 2022 France EnglishPublisher:HAL CCSD Funded by:ANR | INCEPTION, EC | RECoVER, EC | VEOANR| INCEPTION ,EC| RECoVER ,EC| VEOBrault, Antoine; Tran-Kiem, Cécile; Couteaux, Clément; Olié, Valérie; Paireau, Juliette; Yazdanpanah, Yazdan; Ghosn, Jade; Martin-Blondel, Guillaume; Bosetti, Paolo; Cauchemez, Simon;Ending Zero-COVID is challenging, particularly when vaccine coverage is low. Considering Wallis and Futuna, a French Zero-COVID territory affected by reluctance to vaccination, low immunity and high levels of comorbidities, we investigate how targeted use of nirmatrelvir/ritonavir (brand name Paxlovid) can complement vaccination and non-pharmaceutical interventions (NPIs) and mitigate the epidemic rebound expected when Zero-COVID ends.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=od______1398::22c13856e0fd9de1f4691780267f613b&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint , Article 2022 France, SwitzerlandPublisher:Cold Spring Harbor Laboratory Funded by:EC | HBP SGA3, ANR | INCEPTIONEC| HBP SGA3 ,ANR| INCEPTIONGuilherme Dias de Melo; Victoire Perraud; Flavio Alvarez; Alba Vieites-Prado; Seonhee Kim; Lauriane Kergoat; Anthony Coleon; Bettina Salome Trüeb; Magali Tichit; Aurèle Piazza; Agnès Thierry; David Hardy; Nicolas Wolff; Sandie Munier; Romain Koszul; Etienne Simon-Lorière; Volker Thiel; Marc Lecuit; Pierre-Marie Lledo; Nicolas Renier; Florence Larrous; Hervé Bourhy;pmid: 38049391
pmc: PMC10372078
SUMMARYAnosmia was identified as a hallmark of COVID-19 early in the pandemic, however, with the emergence of variants of concern, the clinical profile induced by SARS-CoV-2 infection has changed, with anosmia being less frequent. Here, we assessed the clinical, olfactory and neuroinflammatory conditions of golden hamsters infected with the original Wuhan SARS-CoV-2 strain, its isogenic ORF7-deletion mutant and three variants: Gamma, Delta, and Omicron/BA.1. We show that infected animals developed a variant-dependent clinical disease including anosmia, and that the ORF7 of SARS-CoV-2 contributes to the induction of olfactory dysfunction. Conversely, all SARS- CoV-2 variants were found to be neuroinvasive, regardless of the clinical presentation they induce. Taken together, this confirms that neuroinvasion and anosmia are independent phenomena upon SARS-CoV-2 infection. Using newly generated nanoluciferase-expressing SARS-CoV-2, we validated the olfactory pathway as a major entry point into the brainin vivoand demonstratedin vitrothat SARS-CoV-2 travels retrogradely and anterogradely along axons in microfluidic neuron-epithelial networks.Graphical abstract
https://doi.org/10.4... arrow_drop_down Bern Open Repository and Information System (BORIS)Article . 2023 . Peer-reviewedData sources: Bern Open Repository and Information System (BORIS)HAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/2022.08.31.505985&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesgold 9 citations 9 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert https://doi.org/10.4... arrow_drop_down Bern Open Repository and Information System (BORIS)Article . 2023 . Peer-reviewedData sources: Bern Open Repository and Information System (BORIS)HAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/2022.08.31.505985&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint 2022 FrancePublisher:Research Square Platform LLC Funded by:ANR | INCEPTION, EC | RECoVERANR| INCEPTION ,EC| RECoVERAuthors: SIMON-LORIERE, Etienne; Montagutelli, Xavier; Lemoine, Frederic; Donati, Flora; +49 AuthorsSIMON-LORIERE, Etienne; Montagutelli, Xavier; Lemoine, Frederic; Donati, Flora; Touret, Franck; Bourret, Jerome; Prot, Matthieu; Munier, Sandie; Attia, Mikael; Conquet, Laurine; Nguyen, Scott; amara, faustine; Maisa, Anna; Fournier, Lucie; Brisbarre, Angela; dehan, oceane; Levillayer, Laurine; Gunalan, Vithiagaran; Fonager, Jannik; Rasmussen, Morten; Kemeny, Stephan; Zrhidri, Abdelali; Duret, Thomas; Behillil, Sylvie; Enouf, Vincent; Rodriguez, Christophe; Fourati, Slim; Pawlotsky, Jean-Michel; Capron, Nicolas; Leroy, Hugues; Alessandri-Gradt, Elodie; Juszczak, Florian; Gheysen, Laetitia; Brodard, Véronique; Moret, Hélène; Bos, Martine; Welkers, Matthijs; Scholz, Claus; Paraskevopoulou, Sofia; Josset, Laurence; Cervi, Claire; Couzon, Brigitte; Marque-Juillet, Stéphanie; Delaune, Deborah; Khiari, Slim El; Fumey, Julien; Hallouin-Bernard, Marie-Charlotte; Rey, Félix; Yazdanpanah, Yazdan; Coignard, Bruno; de Lamballerie, Xavier; Werf, Sylvie van der; Paquin, Axelle;Abstract Recombination is a crucial process in the evolution of many organisms. Although the evolutionary reasons behind its occurrence in RNA viruses are debated, this phenomenon has been associated with major epidemiological events such as virus host range expansion, antigenic shift or variation in virulence 1,2, and this process occurs frequently in positive strand RNA viruses such as coronaviruses. The SARS-CoV-2 pandemic has been associated with the repeated emergence of variants of concern presenting increased transmissibility, severity or immune escape 3. The recent extensive circulation of Delta worldwide and its subsequent replacement by viruses of the Omicron lineage 4 (BA.1 then BA.2), have created conditions for genetic exchanges between viruses with both genetic diversity and phenotypic specificities 5-7. Here we report the identification and in vitro and in vivo characterization of a Delta-Omicron recombinant in Europe. This recombinant exhibits immune escape properties similar to Omicron, while its behavior in mice expressing the human ACE2 receptor is more similar to Delta. This recombinant provides a unique and natural opportunity to better understand the genotype to phenotype links in SARS-CoV-2.
https://doi.org/10.2... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-IRDPreprint . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.21203/rs.3.rs-1502293/v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu13 citations 13 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert https://doi.org/10.2... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-IRDPreprint . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.21203/rs.3.rs-1502293/v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2022 FrancePublisher:Oxford University Press (OUP) Funded by:EC | VEO, ANR | TheraCoV, ANR | INCEPTION +1 projectsEC| VEO ,ANR| TheraCoV ,ANR| INCEPTION ,EC| RECoVERLayan, Maylis; Gilboa, Mayan; Gonen, Tal; Goldenfeld, Miki; Meltzer, Lilac; Andronico, Alessio; Hozé, Nathanaël; Cauchemez, Simon; Regev-Yochay, Gili;Abstract Several studies have characterized the effectiveness of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. However, estimates of their impact on transmissibility remain limited. Here, we evaluated the impact of isolation and vaccination (7 days after the second dose) on SARS-CoV-2 transmission within Israeli households. From December 2020 to April 2021, confirmed cases were identified among health-care workers of the Sheba Medical Centre and their family members. Recruited households were followed up with repeated PCR for at least 10 days after case confirmation. Data were analyzed using a data augmentation Bayesian framework. A total of 210 households with 215 index cases were enrolled; 269 out of 667 (40%) susceptible household contacts developed a SARS-CoV-2 infection. Of those, 170 (63%) developed symptoms. Compared with unvaccinated and unisolated adult/teenager (aged >12 years) contacts, vaccination reduced the risk of infection among unisolated adult/teenager contacts (relative risk (RR) = 0.21, 95% credible interval (CrI): 0.08, 0.44), and isolation reduced the risk of infection among unvaccinated adult/teenager (RR = 0.12, 95% CrI: 0.06, 0.21) and child contacts (RR = 0.17, 95% CrI: 0.08, 0.32). Infectivity was reduced in vaccinated cases (RR = 0.25, 95% CrI: 0.06, 0.77). Within households, vaccination reduces both the risk of infection and of transmission if infected. When contacts were unvaccinated, isolation also led to important reductions in the risk of transmission.
American Journal of ... arrow_drop_down American Journal of EpidemiologyArticle . 2022 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-04095187/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/aje/kwac042&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routeshybrid 25 citations 25 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert American Journal of ... arrow_drop_down American Journal of EpidemiologyArticle . 2022 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-04095187/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2022 FrancePublisher:Springer Science and Business Media LLC Funded by:ANR | INCEPTION, EC | RECoVERANR| INCEPTION ,EC| RECoVERAuthors: Xavier Montagutelli; Sylvie van der Werf; Felix A Rey; Etienne Simon‐Loriere;Xavier Montagutelli; Sylvie van der Werf; Felix A Rey; Etienne Simon‐Loriere;International audience; SARS-CoV-2 Omicron harbors substitutions in the receptor binding domain of the spike which strongly suggest its capacity to infect rodents. Wild animal reservoirs could favor the emergence of new variants with risks of spillback to humans and should be closely monitored
EMBO Molecular Medic... arrow_drop_down HAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess Routesgold 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert EMBO Molecular Medic... arrow_drop_down HAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2022 FrancePublisher:Springer Science and Business Media LLC Funded by:EC | VEO, ANR | INCEPTION, EC | RECoVEREC| VEO ,ANR| INCEPTION ,EC| RECoVERBosetti, Paolo; Tran Kiem, Cécile; Andronico, Alessio; Colizza, Vittoria; Yazdanpanah, Yazdan; Fontanet, Arnaud; Benamouzig, Daniel; Cauchemez, Simon;Abstract Background Vaccination is expected to change the epidemiology and management of SARS-CoV-2 epidemics. Methods We used an age-stratified compartmental model calibrated to French data to anticipate these changes and determine implications for the control of an autumn epidemic. We assumed vaccines reduce the risk of hospitalization, infection, and transmission if infected by 95%, 60%, and 50%, respectively. Results In our baseline scenario characterized by basic reproduction number R0=5 and a vaccine coverage of 70–80–90% among 12–17, 18–59, and ≥ 60 years old, important stress on healthcare is expected in the absence of measures. Unvaccinated adults ≥60 years old represent 3% of the population but 43% of hospitalizations. Given limited vaccine coverage, children aged 0–17 years old represent a third of infections and are responsible for almost half of transmissions. Unvaccinated individuals have a disproportionate contribution to transmission so that measures targeting them may help maximize epidemic control while minimizing costs for society compared to non-targeted approaches. Of all the interventions considered including repeated testing and non-pharmaceutical measures, vaccination of the unvaccinated is the most effective. Conclusions With the Delta variant, vaccinated individuals are well protected against hospitalization but remain at risk of infection and should therefore apply protective behaviors (e.g., mask-wearing). Targeting non-vaccinated individuals may maximize epidemic control while minimizing costs for society. Vaccinating children protects them from the deleterious effects of non-pharmaceutical measures. Control strategies should account for the changing SARS-CoV-2 epidemiology.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2022Full-Text: http://europepmc.org/articles/PMC8789481Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BYFull-Text: https://hal.science/hal-03906324v3/documentHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotPreprint . 2021License: CC BY NC NDadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 13 citations 13 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2022Full-Text: http://europepmc.org/articles/PMC8789481Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BYFull-Text: https://hal.science/hal-03906324v3/documentHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotPreprint . 2021License: CC BY NC NDadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2022 FrancePublisher:European Centre for Disease Control and Prevention (ECDC) Funded by:EC | VEO, ANR | INCEPTION, EC | RECoVEREC| VEO ,ANR| INCEPTION ,EC| RECoVERBosetti, Paolo; Tran Kiem, Cécile; Andronico, Alessio; Paireau, Juliette; Levy-Bruhl, Daniel; Alter, Lise; Fontanet, Arnaud; Cauchemez, Simon;Europe has experienced a large COVID-19 wave caused by the Delta variant in winter 2021/22. Using mathematical models applied to Metropolitan France, we find that boosters administered to ≥ 65, ≥ 50 or ≥ 18 year-olds may reduce the hospitalisation peak by 25%, 36% and 43% respectively, with a delay of 5 months between second and third dose. A 10% reduction in transmission rates might further reduce it by 41%, indicating that even small increases in protective behaviours may be critical to mitigate the wave.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2022Full-Text: http://europepmc.org/articles/PMC8739339Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2022Full-Text: http://europepmc.org/articles/PMC8739339Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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description Publicationkeyboard_double_arrow_right Article , Preprint 2022 FrancePublisher:Cold Spring Harbor Laboratory Funded by:NIH | Inter-regional study of t..., EC | EVA-GLOBAL, ANR | INCEPTION +2 projectsNIH| Inter-regional study of transmission, adaptation and pathogenesis of viruses with pandemic potential in Southeast Asia and West/Central Africa ,EC| EVA-GLOBAL ,ANR| INCEPTION ,EC| RECoVER ,EC| EVAgFranck Touret; Emilie Giraud; Jérôme Bourret; Flora Donati; Jaouen Tran-Rajau; Jeanne Chiaravalli; Frédéric Lemoine; Fabrice Agou; Etienne Simon-Lorière; Sylvie van der Werf; Xavier de Lamballerie;SummaryThe landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple sub-variants originating from BA.2, BA.4 and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1 and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1 and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1 and XBB variants.
iScience arrow_drop_down HAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-IRDArticle . 2023License: CC BY NC NDadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess Routesgold 15 citations 15 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!more_vert iScience arrow_drop_down HAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-IRDArticle . 2023License: CC BY NC NDadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publication2022 France EnglishPublisher:HAL CCSD Funded by:EC | VEO, ANR | INCEPTION, EC | RECoVER +1 projectsEC| VEO ,ANR| INCEPTION ,EC| RECoVER ,ANR| TheraCoVAuthors: Layan, Maylis;Layan, Maylis;Parmi les méthodes pour l'étude quantitative de la transmission des maladies infectieuses dans les populations, les épidémiologistes ont récemment focalisé leur attention sur l'épidémiologie moléculaire qui vise à reconstruire la phylogénie des pathogènes en utilisant leurs séquences génétiques, et la modélisation mathématique des maladies infectieuses qui ajuste des modèles mécanistes de transmission des maladies à des données épidémiologiques telles que le nombre de cas. Ces deux approches se basent sur des données très différentes dont la disponibilité varie selon le contexte. Les concepts et les modèles qu'elles utilisent permettent d'explorer des facettes différentes de la transmission des maladies. L'objectif principal de cette thèse est de mieux comprendre comment les maladies virales comme la rage et la covid-19 circulent dans les populations hôtes en utilisant pour la première des séquences génétiques virales datées et géolocalisées, et pour la deuxième, des données épidémiologiques à l'échelle individuelle. La première partie de cette thèse s'intéresse à la rage, une zoonose tropicale négligée, responsable d'environ 59,000 morts chaque année principalement dans les populations pauvres et rurales d'Afrique et d'Asie. Son agent étiologique, le virus de la rage (RABV), circule principalement dans les populations canines domestiques dont les modes de transmission restent peu étudiés et mal compris malgré l'existence de vaccins efficaces chez l'homme et l'animal. Nous avons tout d'abord synthétisé dans une revue de la littérature l'apport relatif des modèles mathématiques et de l'épidémiologie moléculaire dans la compréhension des dynamiques de la rage chez le chien. Puis, nous avons décrit la circulation endémique de la rage au Cambodge, un des pays les plus affectés, à partir de génomes de la rage isolés chez le chien et analysés avec des méthodes de phylogéographie Bayésienne continue. Nous avons montré que les introductions depuis d'autres pays ne sont pas nécessaires au maintien de la circulation. Toutefois, ces résultats sont conditionnés par l'échantillonnage des génomes. Pour mieux comprendre leurs impacts sur les méthodes de phylogéographie Bayésienne, nous avons entrepris une étude de simulation dans laquelle nous avons comparé les performances de trois algorithmes de phylogéographie discrète face à un échantillonnage plus ou moins biaisé. Nous avons testé des stratégies d'échantillonnage alternatives et intégré des données épidémiologiques afin d'atténuer l'effet potentiel des biais d'échantillonnage sur la performance des trois algorithmes. La deuxième partie de la thèse se concentre sur la transmission du SARS-CoV-2 dans une des plus petites populations, les ménages. Cette configuration est particulièrement adaptée au suivi détaillé de l'ensemble des membres du foyer après l'introduction d'un cas et permet ainsi d'évaluer comment la susceptibilité et l'infectivité varient au niveau individuel. Dans un premier temps, nous avons estimé l'effectivité vaccinale contre l'infection et la transmission si infecté pendant la vague de variant Alpha en Israël grâce à un modèle de transmission dans des ménages partiellement vaccinés. Nous avons ensuite exploré comment l'hétérogénéité de contact dans les ménages, notamment entre les adultes et les enfants, impacte les estimations de l'infectivité et de la susceptibilité relatives des enfants par rapport aux adultes. En conclusion, cette thèse explore les contributions de l'épidémiologie moléculaire et de la modélisation pour la compréhension de la transmission des maladies infectieuses à différentes échelles de population et souligne la nécessité d'intégrer les données génétiques et épidémiologiques. Among the methods for the quantitative study of infectious diseases transmission in host populations, molecular epidemiology that reconstructs pathogen phylogenies by using pathogen genetic sequences and mathematical modelling of infectious diseases that fits mechanistic models of disease transmission to epidemiological data such as case counts are of particular interest to epidemiologists. These two approaches rely on different data sources whose availability depends on the setting. They also rely on different concepts and models leading to complementary pictures of disease transmission. The main objective of this thesis is to better understand how viral infectious diseases such as rabies and COVID-19 circulate in host populations using respectively geolocated and timestamped viral genetic sequences and detailed epidemiological data at the individual level. The first part of this thesis focuses on rabies, a neglected tropical zoonosis, that is estimated to cause 59,000 human deaths per year mostly among rural and poor populations in Africa and Asia. Its causing agent, rabies virus (RABV), mainly circulates in domestic dog populations. Despite being a vaccine-preventable disease in both humans and dogs, rabies remains poorly studied and its circulation in dogs poorly understood. First, we reviewed from the literature all mathematical models and molecular epidemiology studies on dog rabies circulation to synthesize the contribution of both approaches to the understanding of rabies dynamics in dogs. Then, we described RABV spread in Cambodia, one of the most affected countries worldwide, using RABV genomes isolated from dogs and Bayesian continuous phylogeography methods. We used Cambodia as a model of endemic circulation of RABV and exemplified how phylogeography can help characterize circulation in such context. We found that introductions from foreign countries are not necessary to sustain transmission in Cambodia. However, these results are conditional on the sampling of the RABV genomes. To further understand how sampling affects Bayesian phylogeography methods, we performed a simulation study where we evaluated the performances of three Bayesian discrete phylogeography algorithms under increasing levels of bias, and tested whether alternative sampling strategies, and integration of incidence data improve the performances of the algorithms under biased sampling conditions. The second part of this thesis concentrates on SARS-CoV-2 transmission at one of the smallest population scale, households. This setting is particularly suitable to detailed follow-up of household members after introduction of a case, and thus, enables to evaluate how susceptibility and infectivity vary between individuals. First, we estimated BNT162b2 vaccine effectiveness against infection and against transmission if infected during the Alpha wave in Israel using a mathematical model of SARS-CoV-2 transmission in partially vaccinated households. We further explored how model misspecification in a context of differing contact patterns between adults and children would impact estimates of relative infectivity and susceptibility of children compared to adults. Overall, this thesis explores how molecular epidemiology and modelling contribute to the understanding of infectious diseases transmission at the population level and highlights the need for data integration.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert HAL-Pasteur arrow_drop_down All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=dedup_wf_002::e81215a3f9f0bb1ca02005b18fc5fa00&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2022 Belgium, France, SpainPublisher:Cold Spring Harbor Laboratory Funded by:NIH | Inter-regional study of t..., ANR | INCEPTION, EC | EVAg +1 projectsNIH| Inter-regional study of transmission, adaptation and pathogenesis of viruses with pandemic potential in Southeast Asia and West/Central Africa ,ANR| INCEPTION ,EC| EVAg ,EC| EVADERAuthors: Delphine Planas; Timothée Bruel; Isabelle Staropoli; Florence Guivel-Benhassine; +21 AuthorsDelphine Planas; Timothée Bruel; Isabelle Staropoli; Florence Guivel-Benhassine; Françoise Porrot; Piet Maes; Ludivine Grzelak; Matthieu Prot; Said Mougari; Cyril Planchais; Julien Puech; Madelina Saliba; Riwan Sahraoui; Florent Fémy; Nathalie Morel; Jérémy Dufloo; Rafael Sanjuán; Hugo Mouquet; Emmanuel André; Laurent Hocqueloux; Etienne Simon-Loriere; David Veyer; Thierry Prazuck; Hélène Péré; Olivier Schwartz;handle: 10261/283495
pmc: PMC9681044 , PMC9926440
Convergent evolution of SARS-CoV-2 Omicron BA.2, BA.4 and BA.5 lineages has led to the emergence of several new subvariants, including BA.2.75.2, BA.4.6. and BQ.1.1. The subvariants BA.2.75.2 and BQ.1.1 are expected to become predominant in many countries in November 2022. They carry an additional and often redundant set of mutations in the spike, likely responsible for increased transmissibility and immune evasion. Here, we established a viral amplification procedure to easily isolate Omicron strains. We examined their sensitivity to 6 therapeutic monoclonal antibodies (mAbs) and to 72 sera from Pfizer BNT162b2-vaccinated individuals, with or without BA.1/BA.2 or BA.5 breakthrough infection. Ronapreve (Casirivimab and Imdevimab) and Evusheld (Cilgavimab and Tixagevimab) lost any antiviral efficacy against BA.2.75.2 and BQ.1.1, whereas Xevudy (Sotrovimab) remained weakly active. BQ.1.1 was also resistant to Bebtelovimab. Neutralizing titers in triply vaccinated individuals were low to undetectable against BQ.1.1 and BA.2.75.2, 4 months after boosting. A BA.1/BA.2 breakthrough infection increased these titers, which remained about 18-fold lower against BA.2.75.2 and BQ.1.1, than against BA.1. Reciprocally, a BA.5 breakthrough infection increased more efficiently neutralization against BA.5 and BQ.1.1 than against BA.2.75.2. Thus, the evolution trajectory of novel Omicron subvariants facilitated their spread in immunized populations and raises concerns about the efficacy of most currently available mAbs. No
Nature Communication... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICPreprint . 2022HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEAArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 101 citations 101 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 36visibility views 36 download downloads 115 Powered bymore_vert Nature Communication... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICPreprint . 2022HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEAArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint 2022 France EnglishPublisher:HAL CCSD Funded by:ANR | INCEPTION, EC | RECoVER, EC | VEOANR| INCEPTION ,EC| RECoVER ,EC| VEOBrault, Antoine; Tran-Kiem, Cécile; Couteaux, Clément; Olié, Valérie; Paireau, Juliette; Yazdanpanah, Yazdan; Ghosn, Jade; Martin-Blondel, Guillaume; Bosetti, Paolo; Cauchemez, Simon;Ending Zero-COVID is challenging, particularly when vaccine coverage is low. Considering Wallis and Futuna, a French Zero-COVID territory affected by reluctance to vaccination, low immunity and high levels of comorbidities, we investigate how targeted use of nirmatrelvir/ritonavir (brand name Paxlovid) can complement vaccination and non-pharmaceutical interventions (NPIs) and mitigate the epidemic rebound expected when Zero-COVID ends.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=od______1398::22c13856e0fd9de1f4691780267f613b&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint , Article 2022 France, SwitzerlandPublisher:Cold Spring Harbor Laboratory Funded by:EC | HBP SGA3, ANR | INCEPTIONEC| HBP SGA3 ,ANR| INCEPTIONGuilherme Dias de Melo; Victoire Perraud; Flavio Alvarez; Alba Vieites-Prado; Seonhee Kim; Lauriane Kergoat; Anthony Coleon; Bettina Salome Trüeb; Magali Tichit; Aurèle Piazza; Agnès Thierry; David Hardy; Nicolas Wolff; Sandie Munier; Romain Koszul; Etienne Simon-Lorière; Volker Thiel; Marc Lecuit; Pierre-Marie Lledo; Nicolas Renier; Florence Larrous; Hervé Bourhy;pmid: 38049391
pmc: PMC10372078
SUMMARYAnosmia was identified as a hallmark of COVID-19 early in the pandemic, however, with the emergence of variants of concern, the clinical profile induced by SARS-CoV-2 infection has changed, with anosmia being less frequent. Here, we assessed the clinical, olfactory and neuroinflammatory conditions of golden hamsters infected with the original Wuhan SARS-CoV-2 strain, its isogenic ORF7-deletion mutant and three variants: Gamma, Delta, and Omicron/BA.1. We show that infected animals developed a variant-dependent clinical disease including anosmia, and that the ORF7 of SARS-CoV-2 contributes to the induction of olfactory dysfunction. Conversely, all SARS- CoV-2 variants were found to be neuroinvasive, regardless of the clinical presentation they induce. Taken together, this confirms that neuroinvasion and anosmia are independent phenomena upon SARS-CoV-2 infection. Using newly generated nanoluciferase-expressing SARS-CoV-2, we validated the olfactory pathway as a major entry point into the brainin vivoand demonstratedin vitrothat SARS-CoV-2 travels retrogradely and anterogradely along axons in microfluidic neuron-epithelial networks.Graphical abstract
https://doi.org/10.4... arrow_drop_down Bern Open Repository and Information System (BORIS)Article . 2023 . Peer-reviewedData sources: Bern Open Repository and Information System (BORIS)HAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/2022.08.31.505985&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesgold 9 citations 9 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert https://doi.org/10.4... arrow_drop_down Bern Open Repository and Information System (BORIS)Article . 2023 . Peer-reviewedData sources: Bern Open Repository and Information System (BORIS)HAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/2022.08.31.505985&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint 2022 FrancePublisher:Research Square Platform LLC Funded by:ANR | INCEPTION, EC | RECoVERANR| INCEPTION ,EC| RECoVERAuthors: SIMON-LORIERE, Etienne; Montagutelli, Xavier; Lemoine, Frederic; Donati, Flora; +49 AuthorsSIMON-LORIERE, Etienne; Montagutelli, Xavier; Lemoine, Frederic; Donati, Flora; Touret, Franck; Bourret, Jerome; Prot, Matthieu; Munier, Sandie; Attia, Mikael; Conquet, Laurine; Nguyen, Scott; amara, faustine; Maisa, Anna; Fournier, Lucie; Brisbarre, Angela; dehan, oceane; Levillayer, Laurine; Gunalan, Vithiagaran; Fonager, Jannik; Rasmussen, Morten; Kemeny, Stephan; Zrhidri, Abdelali; Duret, Thomas; Behillil, Sylvie; Enouf, Vincent; Rodriguez, Christophe; Fourati, Slim; Pawlotsky, Jean-Michel; Capron, Nicolas; Leroy, Hugues; Alessandri-Gradt, Elodie; Juszczak, Florian; Gheysen, Laetitia; Brodard, Véronique; Moret, Hélène; Bos, Martine; Welkers, Matthijs; Scholz, Claus; Paraskevopoulou, Sofia; Josset, Laurence; Cervi, Claire; Couzon, Brigitte; Marque-Juillet, Stéphanie; Delaune, Deborah; Khiari, Slim El; Fumey, Julien; Hallouin-Bernard, Marie-Charlotte; Rey, Félix; Yazdanpanah, Yazdan; Coignard, Bruno; de Lamballerie, Xavier; Werf, Sylvie van der; Paquin, Axelle;Abstract Recombination is a crucial process in the evolution of many organisms. Although the evolutionary reasons behind its occurrence in RNA viruses are debated, this phenomenon has been associated with major epidemiological events such as virus host range expansion, antigenic shift or variation in virulence 1,2, and this process occurs frequently in positive strand RNA viruses such as coronaviruses. The SARS-CoV-2 pandemic has been associated with the repeated emergence of variants of concern presenting increased transmissibility, severity or immune escape 3. The recent extensive circulation of Delta worldwide and its subsequent replacement by viruses of the Omicron lineage 4 (BA.1 then BA.2), have created conditions for genetic exchanges between viruses with both genetic diversity and phenotypic specificities 5-7. Here we report the identification and in vitro and in vivo characterization of a Delta-Omicron recombinant in Europe. This recombinant exhibits immune escape properties similar to Omicron, while its behavior in mice expressing the human ACE2 receptor is more similar to Delta. This recombinant provides a unique and natural opportunity to better understand the genotype to phenotype links in SARS-CoV-2.
https://doi.org/10.2... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-IRDPreprint . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eu13 citations 13 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert https://doi.org/10.2... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-IRDPreprint . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.21203/rs.3.rs-1502293/v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2022 FrancePublisher:Oxford University Press (OUP) Funded by:EC | VEO, ANR | TheraCoV, ANR | INCEPTION +1 projectsEC| VEO ,ANR| TheraCoV ,ANR| INCEPTION ,EC| RECoVERLayan, Maylis; Gilboa, Mayan; Gonen, Tal; Goldenfeld, Miki; Meltzer, Lilac; Andronico, Alessio; Hozé, Nathanaël; Cauchemez, Simon; Regev-Yochay, Gili;Abstract Several studies have characterized the effectiveness of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. However, estimates of their impact on transmissibility remain limited. Here, we evaluated the impact of isolation and vaccination (7 days after the second dose) on SARS-CoV-2 transmission within Israeli households. From December 2020 to April 2021, confirmed cases were identified among health-care workers of the Sheba Medical Centre and their family members. Recruited households were followed up with repeated PCR for at least 10 days after case confirmation. Data were analyzed using a data augmentation Bayesian framework. A total of 210 households with 215 index cases were enrolled; 269 out of 667 (40%) susceptible household contacts developed a SARS-CoV-2 infection. Of those, 170 (63%) developed symptoms. Compared with unvaccinated and unisolated adult/teenager (aged >12 years) contacts, vaccination reduced the risk of infection among unisolated adult/teenager contacts (relative risk (RR) = 0.21, 95% credible interval (CrI): 0.08, 0.44), and isolation reduced the risk of infection among unvaccinated adult/teenager (RR = 0.12, 95% CrI: 0.06, 0.21) and child contacts (RR = 0.17, 95% CrI: 0.08, 0.32). Infectivity was reduced in vaccinated cases (RR = 0.25, 95% CrI: 0.06, 0.77). Within households, vaccination reduces both the risk of infection and of transmission if infected. When contacts were unvaccinated, isolation also led to important reductions in the risk of transmission.
American Journal of ... arrow_drop_down American Journal of EpidemiologyArticle . 2022 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-04095187/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/aje/kwac042&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routeshybrid 25 citations 25 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert American Journal of ... arrow_drop_down American Journal of EpidemiologyArticle . 2022 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-04095187/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/aje/kwac042&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2022 FrancePublisher:Springer Science and Business Media LLC Funded by:ANR | INCEPTION, EC | RECoVERANR| INCEPTION ,EC| RECoVERAuthors: Xavier Montagutelli; Sylvie van der Werf; Felix A Rey; Etienne Simon‐Loriere;Xavier Montagutelli; Sylvie van der Werf; Felix A Rey; Etienne Simon‐Loriere;International audience; SARS-CoV-2 Omicron harbors substitutions in the receptor binding domain of the spike which strongly suggest its capacity to infect rodents. Wild animal reservoirs could favor the emergence of new variants with risks of spillback to humans and should be closely monitored
EMBO Molecular Medic... arrow_drop_down HAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.15252/emmm.202115558&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesgold 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert EMBO Molecular Medic... arrow_drop_down HAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.15252/emmm.202115558&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2022 FrancePublisher:Springer Science and Business Media LLC Funded by:EC | VEO, ANR | INCEPTION, EC | RECoVEREC| VEO ,ANR| INCEPTION ,EC| RECoVERBosetti, Paolo; Tran Kiem, Cécile; Andronico, Alessio; Colizza, Vittoria; Yazdanpanah, Yazdan; Fontanet, Arnaud; Benamouzig, Daniel; Cauchemez, Simon;Abstract Background Vaccination is expected to change the epidemiology and management of SARS-CoV-2 epidemics. Methods We used an age-stratified compartmental model calibrated to French data to anticipate these changes and determine implications for the control of an autumn epidemic. We assumed vaccines reduce the risk of hospitalization, infection, and transmission if infected by 95%, 60%, and 50%, respectively. Results In our baseline scenario characterized by basic reproduction number R0=5 and a vaccine coverage of 70–80–90% among 12–17, 18–59, and ≥ 60 years old, important stress on healthcare is expected in the absence of measures. Unvaccinated adults ≥60 years old represent 3% of the population but 43% of hospitalizations. Given limited vaccine coverage, children aged 0–17 years old represent a third of infections and are responsible for almost half of transmissions. Unvaccinated individuals have a disproportionate contribution to transmission so that measures targeting them may help maximize epidemic control while minimizing costs for society compared to non-targeted approaches. Of all the interventions considered including repeated testing and non-pharmaceutical measures, vaccination of the unvaccinated is the most effective. Conclusions With the Delta variant, vaccinated individuals are well protected against hospitalization but remain at risk of infection and should therefore apply protective behaviors (e.g., mask-wearing). Targeting non-vaccinated individuals may maximize epidemic control while minimizing costs for society. Vaccinating children protects them from the deleterious effects of non-pharmaceutical measures. Control strategies should account for the changing SARS-CoV-2 epidemiology.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2022Full-Text: http://europepmc.org/articles/PMC8789481Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BYFull-Text: https://hal.science/hal-03906324v3/documentHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotPreprint . 2021License: CC BY NC NDadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s12916-022-02235-1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 13 citations 13 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2022Full-Text: http://europepmc.org/articles/PMC8789481Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BYFull-Text: https://hal.science/hal-03906324v3/documentHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotPreprint . 2021License: CC BY NC NDadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s12916-022-02235-1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2022 FrancePublisher:European Centre for Disease Control and Prevention (ECDC) Funded by:EC | VEO, ANR | INCEPTION, EC | RECoVEREC| VEO ,ANR| INCEPTION ,EC| RECoVERBosetti, Paolo; Tran Kiem, Cécile; Andronico, Alessio; Paireau, Juliette; Levy-Bruhl, Daniel; Alter, Lise; Fontanet, Arnaud; Cauchemez, Simon;Europe has experienced a large COVID-19 wave caused by the Delta variant in winter 2021/22. Using mathematical models applied to Metropolitan France, we find that boosters administered to ≥ 65, ≥ 50 or ≥ 18 year-olds may reduce the hospitalisation peak by 25%, 36% and 43% respectively, with a delay of 5 months between second and third dose. A 10% reduction in transmission rates might further reduce it by 41%, indicating that even small increases in protective behaviours may be critical to mitigate the wave.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2022Full-Text: http://europepmc.org/articles/PMC8739339Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.2807/1560-7917.es.2022.27.1.2101125&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2022Full-Text: http://europepmc.org/articles/PMC8739339Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2022License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.2807/1560-7917.es.2022.27.1.2101125&type=result"></script>'); --> </script>
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