Measles in vulnerable populations: An outbreak in Roma settlements of Loire-Atlantique, France, 2019.

In May 2019, a measles outbreak occurred in the French subregion of Loire-Atlantique, particularly affecting Roma settlements. Various obstacles hindered the implementation of postexposure measures among Roma population, resulting in the spread of the cases to other settlements. Suspected cases of measles were immediately investigated and concerned settlements were visited for measles-mumps-rubella (MMR) vaccination. From July 1 to September 3, 2019, a first and then a second Health Reserve team helped for vaccination on the affected and then also the measles-free settlements. Vaccination uptake was monitored with the use of the department's vaccination center immunization registry. Genotyping of selected samples was performed for comparison with viruses circulating at the same time in France and Romania. As of September 16 2019, 109 cases of measles were confirmed among Roma population, including 99 (91%) children under 15 years. Of the 85 people eligible for vaccination, 60 (71%) had not been vaccinated and 23 (27%) had an unknown vaccination status. Sequence comparison revealed that 28/29 sequenced D8 strains were 100% identical to the strain responsible for a large number of cases throughout France in 2019, and to two sequences reported in Romania among sporadic cases. The vaccination campaign resulted in 1136 people on 35 settlements receiving at least one dose of MMR vaccine and in the increase of one-dose MMR vaccine coverage at 24 months from 43% (23/53) to 91% (48/53). With measles transmission continuing in Europe, efforts must be made to meet immunization coverage targets, particularly in hard-to-reach communities where outbreaks may be difficult to control.

Evaluation of a prophylactic transfusion program on obstetric outcomes in pregnant women with sickle cell disease: A single centre retrospective cohort study.

OBJECTIVE: To evaluate the effects of a prophylactic transfusion program (TP) on obstetric and perinatal outcomes in pregnant women with sickle cell disease (SCD). METHODS: This retrospective cohort study included all singleton pregnancies among women with SCD in a French university tertiary care center between 1 January 2004 and 31 December 2017. The TP group included patients selected according to the French guidelines who received regular red blood cell transfusions during pregnancy until delivery. The factors associated with TP indication [year of birth, SCD genotype, history of acute chest syndrome and delayed hemolysis transfusion reaction (DHTR) risk score] were taken into account in a propensity score. A composite obstetric adverse outcome was defined associating birth before 34 gestational weeks and/or pre-eclampsia and/or small for gestational age and/or abruption and/or stillbirth and/or maternal death and/or neonatal death. RESULTS: In total, 246 pregnancies in 173 patients were analyzed. Twenty-two pregnancies with a history of DHTR were excluded. A higher frequency of TP was found before 2013 [119/148 (80.4%) vs 38/76 (50%); p < 0.001]. Rates of preterm birth before 34 gestational weeks (5.6% vs 19.7%; p = 0.001), vaso-occlusive crisis (36.5% vs. 61.8%; p < 0.001), and acute chest syndrome (6.1% vs. 14.5%; p = 0.04) during pregnancy were decreased significantly in the TP group. Among the groups with and without composite obstetric adverse outcomes, the frequency of TP was 52.6% and 74.7%, respectively [odds ratio (OR) 0.30, 95% confidence interval (CI) 0.09-1.02]. The multivariate analysis shows that the TP was associated with a significant reduction in the risk of composite obstetric adverse outcomes (OR 0.28, 95% CI 0.08-0.97; p = 0.04). CONCLUSION: A red blood cell TP may have an independent protective effect on maternal and perinatal adverse outcomes during pregnancy in women with SCD.

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.

Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and accuracy on simulated data, where it performs better than the state-of-the-art methods. To illustrate its applicability, we assess the dynamics induced by superspreading individuals in an HIV dataset of men-having-sex-with-men in Zurich. Our tool PhyloDeep is available on github.com/evolbioinfo/phylodeep .

Follow-up of Intracranial Aneurysms Treated by Flow Diverters: Evaluation of Parent Artery Patency Using 3D-T1 Gradient Recalled-Echo Imaging with 2-Point Dixon in Combination with 3D-TOF-MRA with Compressed Sensing.

BACKGROUND AND PURPOSE: MRA assessment of parent artery patency after flow-diverter placement is complicated by imaging artifacts produced by these devices. The purpose of this study was to assess the accuracy of liver acquisition with volume acceleration-flex technique (LAVA-Flex) MRA in combination with 3D-TOF with HyperSense MRA for the evaluation of parent vessel status after intracranial flow-diverter placement. MATERIALS AND METHODS: Fifty-six patients treated by flow diversion and followed with both DSA and 3T MRA between November 2020 and August 2021 were included. All patients were evaluated for parent artery patency using the same imaging protocol (DSA, noncontrast MRA including 3D-TOF with HyperSense and LAVA-Flex, and contrast-enhanced MRA, including time-resolved imaging of contrast kinetics MRA and delayed contrast-enhanced MRA). RESULTS: With DSA as a criterion standard to evaluate the patency of the parent vessel, noncontrast MRA had a good specificity (0.83) and positive predictive value (0.65), better than contrast-enhanced MRA (0.55 and 0.41, respectively). Both had excellent sensitivity and negative predictive value: noncontrast MRA, 0.93 and 0.97, respectively; contrast-enhanced MRA, 0.93 and 0.96, respectively. Specificity and positive predictive value tended to be lower for patients treated with additional devices than for those treated with flow diverters exclusively and for patients treated with a specific type of flow diverter. CONCLUSIONS: Noncontrast MRA can be used for noninvasive follow-up of intracranial aneurysms treated by flow diverters. The combined use of LAVA-Flex and 3D-TOF with HyperSense sequences allows monitoring the status of the parent artery and aneurysm occlusion.

COVID-19 vaccines: Frequently asked questions and updated answers.

At the end of December 2019, China notified the World Health Organization about a viral pneumonia epidemic soon to be named COVID-19, of which the infectious agent, SARS-CoV-2, was rapidly identified. Less than one year later, published phase 3 clinical trials underlined the effectiveness of vaccines utilizing hitherto unusual technology consisting in injection of the messenger RNA (m-RNA) of a viral protein. In the meantime, numerous clinical trials had failed to identify a maximally effective antiviral treatment, and mass vaccination came to be considered as the strategy most likely to put an end to the pandemic. The objective of this text is to address and hopefully answer the questions being put forward by healthcare professionals on the different anti-SARS-CoV-2 vaccines as regards their development, their modes of action, their effectiveness, their limits, and their utilization in different situations; we are proposing a report on both today's state of knowledge, and the 14 February 2021 recommendations of the French health authorities.

Large-scale regulatory and signaling network assembly through linked open data.

Huge efforts are currently underway to address the organization of biological knowledge through linked open databases. These databases can be automatically queried to reconstruct regulatory and signaling networks. However, assembling networks implies manual operations due to source-specific identification of biological entities and relationships, multiple life-science databases with redundant information and the difficulty of recovering logical flows in biological pathways. We propose a framework based on Semantic Web technologies to automate the reconstruction of large-scale regulatory and signaling networks in the context of tumor cells modeling and drug screening. The proposed tool is pyBRAvo (python Biological netwoRk Assembly), and here we have applied it to a dataset of 910 gene expression measurements issued from liver cancer patients. The tool is publicly available at https://github.com/pyBRAvo/pyBRAvo.

Cryptosporidium-Biofilm Interactions: a Review.

Biofilms are increasingly implicated as playing a major role in waterborne cryptosporidiosis. This review aims to synthesize all currently available data on interactions between Cryptosporidium oocysts and biofilms. Initially described following a waterborne outbreak, the integration of Cryptosporidium oocysts in biofilm has been well demonstrated. Biofilms appear important in the dissemination/protection of oocysts in the environment. Consequently, it has been suggested that substrate-associated biofilms should be systematically considered in oocyst water quality assessment. The influence of physicochemical parameters has been studied on oocyst biofilm retention. Biofilm surface roughness, ionic concentration (especially Ca2+), laminar/turbulent flow, shear stress, and electrostatic repulsion forces appear important to consider regarding oocyst release from biofilm. However, data analysis carried out during this review also revealed important gaps in biological interactions within biofilms, offering many perspectives for future work.

Author Correction: Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.

Guinea pigs (Cavia spp.) have a long association with humans. From as early as 10,000 years ago they were a wild food source. Later, domesticated Cavia porcellus were dispersed well beyond their native range through pre-Columbian exchange networks and, more recently, widely across the globe. Here we present 46 complete mitogenomes of archaeological guinea pigs from sites in Peru, Bolivia, Colombia, the Caribbean, Belgium and the United States to elucidate their evolutionary history, origins and paths of dispersal. Our results indicate an independent centre of domestication of Cavia in the eastern Colombian Highlands. We identify a Peruvian origin for the initial introduction of domesticated guinea pigs (Cavia porcellus) beyond South America into the Caribbean. We also demonstrate that Peru was the probable source of the earliest known guinea pigs transported, as part of the exotic pet trade, to both Europe and the southeastern United States. Finally, we identify a modern reintroduction of guinea pigs to Puerto Rico, where local inhabitants use them for food. This research demonstrates that the natural and cultural history of guinea pigs is more complex than previously known and has implications for other studies regarding regional to global-scale studies of mammal domestication, translocation, and distribution.

Quantitative assessment of sciatic nerve changes in Charcot-Marie-Tooth type 1A patients using magnetic resonance neurography.

BACKGROUND AND PURPOSE: Nerve tissue alterations have rarely been quantified in Charcot-Marie-Tooth type 1A (CMT1A) patients. The aim of the present study was to quantitatively assess the magnetic resonance imaging (MRI) anomalies of the sciatic and tibial nerves in CMT1A disease using quantitative neurography MRI. It was also intended to seek for correlations with clinical variables. METHODS: Quantitative neurography MRI was used in order to assess differences in nerve volume, proton density and magnetization transfer ratio in the lower limbs of CMT1A patients and healthy controls. Disease severity was evaluated using the Charcot-Marie-Tooth Neuropathy Score version 2, Charcot-Marie-Tooth examination scores and Overall Neuropathy Limitations Scale scores. Electrophysiological measurements were performed in order to assess the compound motor action potential and the Motor Unit Number Index. Clinical impairment was evaluated using muscle strength measurements and Charcot-Marie-Tooth examination scores. RESULTS: A total of 32 CMT1A patients were enrolled and compared to 13 healthy subjects. The 3D nerve volume, magnetization transfer ratio and proton density were significantly different in CMT1A patients for the whole sciatic and tibial nerve volume. The sciatic nerve volume was significantly correlated with the whole set of clinical scores whereas no correlation was found between the tibial nerve volume and the clinical scores. CONCLUSION: Nerve injury could be quantified in vivo using quantitative neurography MRI and the corresponding biomarkers were correlated with clinical disability in CMT1A patients. The sensitivity of the selected metrics will have to be assessed through repeated measurements over time during longitudinal studies to evaluate structural nerve changes under treatment.

Complete genome sequence of a novel grapevine-infecting member of the genus Polerovirus, grapevine polerovirus 1.

Double-stranded RNAs and total RNAs purified from grapevine (Vitis vinifera) phloem scrapings of two varieties held in the INRAE (France) grapevine germplasm collection were analyzed by high-throughput sequencing. BLAST annotation revealed contigs with homology to Polerovirus genus members. The full genome sequence of one isolate (KT) was determined (5651 nucleotides [nt]), and a partial sequence representing about half of the genome was assembled for a second isolate (KS) that was found to share 95% nt sequence identity with the KT isolate. The genome has a typical polerovirus organization, containing six open reading frames (ORFs) as well as a putative additional ORF3a. Based on genome organization and phylogenetic relationships, the new virus belongs to the genus Polerovirus but, similar to the recently described persimmon polerovirus 1, is characterized by a highly divergent coat-protein/readthrough domain. Considering the species demarcation criteria for the family Luteoviridae, these two isolates, together with a closely related sequence recently deposited in the GenBank database (LC507098), represent a new Polerovirus species for which the name "Grapevine polerovirus 1" is proposed.

Cryptosporidiosis and microsporidiosis as causes of diarrhea in kidney and/or pancreas transplant recipients.

INTRODUCTION: Gastrointestinal disorders in solid organ recipients may have various origins including cryptosporidiosis and microsporidiosis. The prevalence of these infections is poorly known in solid organ transplant (SOT) patients in industrialized countries. METHODS: We prospectively assessed the infectious causes of diarrhea in SOT patients. Secondary objectives were to gain further insight into the main characteristics of cryptosporidiosis, and to assess risk factors for this infection. All adult kidney and/or pancreas recipients presenting with diarrhea and admitted to our facility between May 1, 2014 and June 30, 2015 were enrolled. A stool sample was analyzed using a standardized protocol including bacteriological, virological, and parasitological investigations. Data related to clinical symptoms, immunosuppression, and environmental potential risk factors were collected through a self-administered questionnaire and computerized medical records. RESULTS: Out of 73 enrolled patients, 36 had infectious diarrhea (49.3%). Viruses ranked first (17/36), followed by parasites and fungi (11/17). Cryptosporidiosis was the most common parasitic disease (n=6 patients). We observed four microsporidiosis cases. The estimated prevalence of cryptosporidiosis and microsporidiosis in this cohort was 3.7 and 2.40/00, respectively. No significant risk factor for cryptosporidiosis or microsporidiosis, neither environmental nor immunological, could be evidenced. CONCLUSION: Both cryptosporidiosis and microsporidiosis represent a significant cause of diarrhea in kidney transplant recipients.

Acceptance of pregnant women's vaccination against pertussis among French women and health professionals: PREVACOQ-1 and -2 studies.

OBJECTIVES: Protection of French young infants against pertussis only relies on their relatives' vaccination. The alternative is vaccination of pregnant women against pertussis (cocooning strategy), but this strategy is not yet recommended in France. We assessed the acceptance of this strategy among French postpartum women and health professionals. PATIENTS AND METHODS: We performed a multicenter survey in 2016 among postpartum women and health professionals (family physicians, obstetricians-gynecologists, midwives, and medical students) to determine the acceptance of anti-pertussis vaccination. We evaluated knowledge, perception, and attitude towards vaccination to identify factors associated with acceptance. RESULTS: Questionnaires were completed by 52% (1208/2337) of women and 40% (694/1754) of health professionals. Seventy-seven per cent of women (95% CI: 74-79) and 93% of health professionals (95% CI: 91-95) were favorable to anti-pertussis vaccination of pregnant women. Thirty-three per cent (227/687) of health professionals believed that pertussis induced life-long immunity and 20% (136/687) of them were not aware of the cocooning strategy. In multivariate analysis, factors associated with acceptance among women were younger age, higher knowledge, having received advice during pregnancy, being vaccinated against influenza, and having never refused any vaccine; among health professionals, factors associated with acceptance were belief that inactivated vaccines are obstetrically safe, regular practice of influenza vaccination in pregnant women, pertussis cocooning strategy, and never prescribing preventive homeopathy for influenza. CONCLUSION: Vaccination of pregnant women against pertussis should be well-accepted by informed mothers and health professionals. If this strategy were to be implemented in France, efforts should be made towards adequate information.

Clinical guidelines for the management of treatment-resistant depression: French recommendations from experts, the French Association for Biological Psychiatry and Neuropsychopharmacology and the fondation FondaMental.

BACKGROUND: Clear guidance for successive antidepressant pharmacological treatments for non-responders in major depression is not well established. METHOD: Based on the RAND/UCLA Appropriateness Method, the French Association for Biological Psychiatry and Neuropsychopharmacology and the fondation FondaMental developed expert consensus guidelines for the management of treatment-resistant depression. The expert guidelines combine scientific evidence and expert clinicians' opinions to produce recommendations for treatment-resistant depression. A written survey comprising 118 questions related to highly-detailed clinical presentations was completed on a risk-benefit scale ranging from 0 to 9 by 36 psychiatrist experts in the field of major depression and its treatments. Key-recommendations are provided by the scientific committee after data analysis and interpretation of the results of the survey. RESULTS: The scope of these guidelines encompasses the assessment of pharmacological resistance and situations at risk of resistance, as well as the pharmacological and psychological strategies in major depression. CONCLUSION: The expert consensus guidelines will contribute to facilitate treatment decisions for clinicians involved in the daily assessment and management of treatment-resistant depression across a number of common and complex clinical situations.

Clinical guidelines for the management of depression with specific comorbid psychiatric conditions French recommendations from experts (the French Association for Biological Psychiatry and Neuropsychopharmacology and the fondation FondaMental).

BACKGROUND: Recommendations for pharmacological treatments of major depression with specific comorbid psychiatric conditions are lacking. METHOD: The French Association for Biological Psychiatry and Neuropsychopharmacology and the fondation FondaMental developed expert consensus guidelines for the management of depression based on the RAND/UCLA Appropriatneness Method. Recommendations for lines of treatment are provided by the scientific committee after data analysis and interpretation of the results of a survey of 36 psychiatrist experts in the field of major depression and its treatments. RESULTS: The expert guidelines combine scientific evidence and expert clinician's opinion to produce recommendations for major depression with comorbid anxiety disorders, personality disorders or substance use disorders and in geriatric depression. CONCLUSION: These guidelines provide direction addressing common clinical dilemmas that arise in the pharmacologic treatment of major depression with comorbid psychiatric conditions.