Evaluer la sélection génomique au sein de croisements bi-parentaux d’espèces pérennes fruitières génotypés par séquençage : point d’étape du projet FruitSelGen

Poste

Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

UMR-AGAP Equipe DAVV (Diversité, adaptation et amélioration de la vigne) ; équipe ID (Intégration de Données)International audienceAbstractBackgroundAs for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. In perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked to agronomic traits variation. However, due to the long juvenile period of these species, establishing numerous highly recombinant populations for high resolution mapping is both costly and time-consuming. Genome wide association studies in germplasm panels is an alternative method of choice, since it allows identifying the main quantitative trait loci with high resolution by exploiting past recombination events between cultivars. Such studies require adequate panel design to represent most of the available genetic and phenotypic diversity. Assessing linkage disequilibrium extent and panel power is also needed to determine the marker density required for association studies.ResultsStarting from the largest grapevine collection worldwide maintained in Vassal (France), we designed a diversity panel of 279 cultivars with limited relatedness, reflecting the low structuration in three genetic pools resulting from different uses (table vs wine) and geographical origin (East vs West), and including the major founders of modern cultivars. With 20 simple sequence repeat markers and five quantitative traits, we showed that our panel adequately captured most of the genetic and phenotypic diversity existing within the entire Vassal collection. To assess linkage disequilibrium extent and panel power, we genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129 distributed over the whole genome. Linkage disequilibrium, measured by correlation corrected for kinship, reached 0.2 for a physical distance between 9 and 458 Kb depending on genetic pool and genomic region, with varying size of linkage disequilibrium blocks. This panel achieved reasonable power to detect associations between traits with high broad-sense heritability (> 0.7) and causal loci with intermediate allelic frequency and strong effect (explaining > 10 % of total variance).ConclusionsOur association panel constitutes a new, highly valuable resource for genetic association studies in grapevine, and deserves dissemination to diverse field and greenhouse trials to gain more insight into the genetic control of many agronomic traits and their interaction with the environment

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Are the conditions met to make COVID-19 vaccination mandatory for healthcare professionals?

International audienceNo abstract availabl

Attitudes towards monkeypox vaccination among healthcare workers in France and Belgium: an element of complacency?

info:eu-repo/semantics/publishe

[i]MybA1[/i] gene diversity across the [i]Vitis[/i] genus

The MybA1 gene in the genus Vitis encodes a transcription factor, belonging to the R2R3 Myb family, that controls the last steps in the anthocyanins biosynthesis pathway. Polymorphism within MybA1 has been associated with color variation in berries of V. vinifera and other Vitis species. In this work, we analyzed the sequence variation in MybA1 both in the subg. Muscadinia and in an extended set of Asian, American and European genotypes of subg. Vitis. Our aims were to infer the evolution of this gene during the speciation process and to identify polymorphisms that could potentially generate changes in gene regulation. The results show that MybA1 experienced many insertions and deletions in non-coding regions but also in the third exon sequence. Owing to the larger set of Vitis species compared here, new indels were identified and the origin of previously described indels was reconsidered. A large number of single nucleotide polymorphisms were found in non-coding regions but also in the sequence coding for the R2R3 domain and the C terminal part of the protein. Some of these changes led to amino acid substitutions and therefore could have modified MybA1 protein activity. Bayesian phylogenetic analysis of all polymorphisms did not provide a consensus tree depicting the geographical partitioning of the species but allowed highlighting several species relationships within subgenus Vitis. Finally, the evolutionary events described could be useful to gain more insight into the role of MybA1 for anthocyanin biosynthesis in grapevine

Vaccines for healthcare-associated infections: present, future, and expectations

Introduction: In spite of the widespread implementation of preventive strategies, the prevalence of healthcare-associated infections (HAIs) remains high. HAIs are associated with multidrug resistant organisms, and in the post-antibiotic era, alternative strategies such as vaccines are needed for their management. Areas covered: Vaccines to prevent HAIs could be proposed to at-risk patients, or to healthcare workers (HCWs) to prevent cross-transmission. After searches in Pubmed and clinicaltrials.gov, existing vaccines and vaccines under clinical development are presented in this narrative review. Issues associated with the use of vaccines to prevent HAIs are discussed. Expert commentary: Future vaccines against HAIs will contribute to fight antibiotic resistance and thus reduce the burden of HAIs. At this stage, the goal of obtaining effective vaccines against S.aureus, C. difficile and gram-negative bacteria has not yet been achieved. Obtaining an efficient response to vaccines in at-risk patients for HAIs is also challenging, and future strategies of vaccination need to address this difficulty. The efficacy of vaccines for HCWs in reducing the spread of nosocomial outbreaks is counterbalanced by the lack of adherence to vaccine policies among HCWs. The acceptance of future vaccines to prevent carriage and infection with organisms involved in HAIs in HCWs will probably be a challenge

Intention to participate in COVID-19 vaccine clinical trials in May 2021: a cross-sectional survey in the general French population

International audienc

Change in self-perceived vaccine confidence in France after the COVID-19 vaccination campaign: A cross-sectional survey in the French general population

International audienceIntroduction: High COVID-19 vaccine coverage was obtained in France after theCOVID-19 vaccination campaign, in part due to the implementation of a COVID-19 vaccination pass, a kind of vaccine mandate. Vaccine mandates could lead to reactance and may affect confidence in vaccines. We aimed to evaluate the impact of the COVID-19 vaccination campaign on self-perceived vaccine confidence in France.Methods: Between the 25th of April and the 9th of May 2022, we conducted a cross-sectional online survey among a representative sample of the French population aged 18 and over. The primary outcome was the perceived change in vaccine confidence after the COVID-19 vaccination campaign. We performed a multinomial regression analysis to identify factors associated with perceived decrease and increase in vaccine confidence in reference to no change.Results: Among the 1,928 respondents, decrease in vaccine confidence was reported by 579 (30 %) and increase in vaccine confidence by 259 (13.4%). Among the 1,711 vaccinated individuals, 693 (40.5%), 404 (23.6%) respectively reported that they felt strongly and a little coerced into getting vaccinated against COVID-19. Younger age, feeling coerced to get vaccinated, low confidence in health authorities, fears about vaccine side effects, and not considering vaccination as a collective responsibility were associated with perceived decrease in vaccine confidence in multivariable analysis. Men were more prone than women to report a gain in vaccine confidence.Conclusion: Vaccination campaign that included coercive measures to raise high COVID-19 vaccine coverage could have led to reactance and with an impact on vaccine confidence in general

Public opinion on a mandatory COVID-19 vaccination policy in France: a cross-sectional survey

International audienc