Nouvelles méthodes de détection de virus dans l'environnement : application à l'identification de nouveaux virus géants dans le milieu marin.

L’objectif de cette thèse était d’isoler de nouveaux Mimiviridae dans l’environnement marin à l’aide d’amibes, hôtes potentiels de ces derniers et surtout organismes ubiquistes phagocytaires et connus pour être parasités par des microorganismes pathogènes. Après la mise en place et la validation de protocoles d’échantillonnages et de mise en culture de prélèvements environnementaux, plusieurs échantillons ont été analysés. Un nouveau membre de la famille des Mimiviridae a été isolé à partir d’un échantillon marin côtier provenant du Chili, stocké dans un milieu enrichi en amidon (milieu riz, propice à la conservation voire à la production de virus) puis mis en coculture dans une souche d’amibe Acanthamoeba griffini. Le séquençage de son génome révèle 1260 kb, codant pour 1120 protéines putatives, ce qui en fait le plus grand génome viral connu. Nommé megavirus chiliensis, sa capside est icosaédrique et possède également des fibrilles comme Acanthamoeba polyphaga mimivirus tout en étant plus grande (diamètre apparent 520 nm vs 450 nm). Bien que les morphologies des deux virus soient similaires et que de nombreuses particularités de mimivirus soient conservées chez megavirus (stargate), 23 % des protéines de megavirus n’ont pas d’homologues chez mimivirus, et les 594 gènes orthologues partagés présentent une identité résiduelle moyenne de 50 %. De plus, megavirus présente 3 amino-acyl-ARNt-synthètases supplémentaires (IleRS, TrpRS et AsnRS) à celles de mimivirus. Ces résultats suggèrent que ces deux virus sont issus d’un génome cellulaire ancestral qui a évolué par réduction génomique. Un parasite intracellulaire obligatoire a également été isolé à partir d’échantillons de sédiments marins de la côte chilienne. Des observations au microscope électronique à transmission indiquent une forme ressemblant à une endospore, de taille très variable (de 400 nm jusqu’à 1 μm), avec une paroi multicouche épaisse (~60 nm) et un pore apical. Cependant, aucune évidence de division n’a encore été observée, laissant penser que cette entité capable de multiplication pourrait être un virus, sans ressembler aux morphologies connues à ce jour.In order to isolate new Mimiviridae from the marine environment, we used amoeba -ubiquitous phagotrophic protozoa - as potential host for these viruses. Different sampling protocols were tested and validated before carrying out co-cultures with amoeba and environmentals samples. A new Mimiviridae giant virus was isolated from Chilean coastal seawater completed with rice media (enriched incubation). Produced in Acanthamoeba griffini, its genome sequence has 1,260 Mbp and encodes for 1120 putative proteins, making it the largest known viral genome and thus named Megavirus chiliensis. Its icosaedral capsid is covered with fibrils and its size is bigger than that of Acanthamoeba polyphaga mimivirus (520 nm vs 450 nm). Although both virions are very similar and most of the mimivirus idiosyncrasies are conserved in megavirus (stargate), 23 % of megavirus putative proteins have no mimivirus homologs. Both viruses share 594 orthologous proteins exhibiting an average identity of 50 %. Moreover, megavirus contains 3 additional amino-acyl tRNA synthetases (IleRS, TrpRS and AsnRS) compare to mimivirus. These results suggest that these viruses have evolved from an ancestral cellular genome by reductive evolution. In addition, an amoeba obligatory intracellular parasite was isolated from marine sediments from Chilean coast. Transmission electron microscopic images show a particule like endospore with variable size (from 400 nm to 1 µm), a multilayered outer wall (~60 nm) and an apical pore. No evidence of division was observed, suggesting that the multiplication of this endoparasite occurs without division, suggesting that it could be a virus without any similarity to those described today

Molecular and distribution data on the poorly known, elusive, cave mysid Harmelinella mariannae (Crustacea: Mysida)

International audienceMediterranean underwater marine caves harbour abundant populations of several species of mysids that are increasingly used as biological models in ecological and evolutionary studies. One exception is the species Harmelinella mariannae, described in 1989 and then hardly ever again reported in the literature. We here provide the first data on the distribution of this poorly known taxon that, contrary to expectations for a rare brooding cave dweller, we now report from Madeira Island in the nearby Atlantic, to the easternmost parts of the Mediterranean. Brief behavioural observations are added, particularly its atypical solitary habits and its feeding behaviour as a high trophic level carnivore. Molecular characterization of the different specimens captured provided three sorts of information. Mitochondrial COI and 16S haplotypes suggest different colonization waves in the Mediterranean, with one group in the Eastern Basin, two in the Marseille region in the NW part of this sea, and another group with a very wide extension from Madeira to Liguria and Malta. Mitochondrial data also support that one of the groups in Marseille might have diverged as a cryptic species of Harmelinella. 18S rRNA gene displays a single common sequence to all specimens from the four groups, and seems to confirm the original proposed placement of this taxon within the subfamily Heteromysinae, not Leptomysinae

Haemophagocytic lymphohistiocytosis in a patient with left ventricular assist device

Left ventricular assist devices provide circulatory support to heart failure patients while awaiting a suitable donor heart. However, with their increased duration of therapy, complications are seen frequently. Although coagulation disorders (bleeding and thrombosis) are the most common complications, infection is also a major complication associated with significant morbidity. We report a case of a 53-year-old male with a left ventricular assist device who presented with driveline infection. He subsequently developed pancytopenia and was diagnosed with haemophagocytosis. Immediate treatment with intravenous immunoglobulin and methylprednisolone was started. His blood cell count returned to normal levels and the patient became eligible for heart transplantation again. Our case represents the rare occurrence of haemophagocytosis in a patient, which, if unnoticed, could lead to fatal consequences

Data from: Cryptic habitats and cryptic diversity: unexpected patterns of connectivity and phylogeographic breaks in a Mediterranean endemic marine cave mysid

The marine cave-dwelling mysid Hemimysis margalefi is distributed over the whole Mediterranean Sea which contrasts with the poor dispersal capabilities of this brooding species. In addition, underwater marine caves are a highly fragmented habitat which further promotes strong genetic structuring, therefore providing highly informative data on the levels of marine population connectivity across biogeographic regions. This study investigates how habitat and geography have shaped the connectivity network of this poor disperser over the entire Mediterranean Sea through the use of several mitochondrial and nuclear markers. Five deeply divergent lineages were observed among H. margalefi populations resulting from deep phylogeographic breaks, some dating back to the Oligo-Miocene. Whether looking at the intra-lineage or inter-lineage levels, H. margalefi populations present a high genetic diversity and population structuring. This study suggests that the five distinct lineages observed in H. margalefi actually correspond to as many separate cryptic taxa. The nominal species, H. margalefi sensu stricto, corresponds to the westernmost lineage here surveyed from the Alboran Sea to south-eastern Italy. Typical genetic breaks such as the Almeria-Oran Front or the Sicilo-Tunisian Strait do not appear to be influential on the studied loci in H. margalefi sensu stricto. Instead, population structuring appears more complex and subtle than usually found for model species with a pelagic dispersal phase. The remaining four cryptic taxa are all found in the eastern basin, but incomplete lineage sorting is suspected and speciation might still be in process. Present day population structure of the different H. margalefi cryptic species appears to result from past vicariance events started in the Oligo-Miocene and maintained by present day coastal topography, water circulation and habitat fragmentation

RSV prevention and treatment in pediatric lung transplant patients: a survey of current practices among the International Pediatric Lung Transplant Collaborative

RSV infection can be severe after pediatric lung transplantation. Strategies to prevent and treat RSV in this population are underreported. To assess the current practices, we surveyed the members of the IPLTC regarding RSV prevention and treatment strategies. Twenty-eight programs were surveyed; 18 (64.3%) responded at least partially. A median of 53 transplants (range, 8-355) occurred since inception. RSV testing occurs in asymptomatic (6/17) and symptomatic (17/17) patients. Diagnostic method is polymerase chain reaction at 13 sites and DFA at 8. Transplant candidates were received prophylaxis at 10 sites, with nine following national (5) or local (4) guidelines. All use palivizumab IM and/or IV. Recipients were received prophylaxis with palivizumab at eight centers (eight IM, one IV). Fourteen were treated for RSV (seven all patients; seven age-related). Medications include inhaled (6), oral (4), or IV (4) ribavirin, plus IVIG (9), steroids (8), and IV (2) or IM (3) palivizumab. Prevention and treatment barriers include insurance/hospital concerns, such as institutional reluctance to use inhaled ribavirin. RSV prevention and treatment strategies are diverse at pediatric lung transplant programs. Many centers offer prophylaxis (9/17) and treatments (14/17), but strategies are not uniform

Hemimysismargalefi-MolEcol-Phylogeo

Data files and tree files for assessing the phylogeography of Hemimysis margalefi in the Mediterranean Se

Epidemiologic, Clinical and Laboratory Features of Pandemic Influenza (H1N1) 2009 Virus Infection

Introduction: After the definition of the first H1N1 case on 15 April 2009, the first case in our country was reported on 15 May 2009, and the first local case was seen on 18 June 2009. In this study, we evaluated patients hospitalized with a pre-diagnosis of H1N1 virus infection, according to epidemiologic, clinical and laboratory features. Materials and Methods: Cases hospitalized between October 2009 and January 2010 with a pre-diagnosis of pandemic influenza and for whom samples of nasal and oropharyngeal swabs were obtained were included in the study. Epidemiologic and laboratory properties of the cases (for both H1N1 positive and H1N1negative groups) were evaluated, as well as their prognoses and treatment. Results: Between October 2009 and January 2010, 155 patients with pre-diagnoses of H1N1 were hospitalized. Eighty-four H1N1 positive and 71 H1N1 negative patients were evaluated. Cough, fatigue and fever were the most frequently observed symptoms. Obesity, fatigue and diarrhea were more common in the H1N1 negative group. Abnormal chest X-ray, lymphopenia and leukopenia were more common in the H1N1 positive group. The fatality rate was determined as 7.1%. 21.4% of the patients (18/84) required intensive care. Twelve patients were monitored with invasive and 3 with non-invasive mechanical ventilation. None of the patients in the H1N1 negative group required intensive care. In the H1N1 positive group, 69 patients received oseltamivir and 47 patients received oseltamivir and antibiotherapy. Conclusion: The new pandemic influenza virus came under the spotlight because of its fast spread and the complications seen in young patients with no comorbidities, where normally influenza-related complications are not expected. The majority of our cases were young adult patients. Most of the cases hospitalized with H1N1 diagnosis had symptoms similar to pneumonia, low oxygen saturation and deterioration in their general condition. Antiviral treatment initiated during the early phases of the disease was successful. Respiratory support and intensive care play a vital role in the cases in which they are needed. Informing the population about the disease and educating them on its transmission and immunization are very important in preventing its spread

Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes

International audienceTen years ago, the discovery of Mimivirus, a virus infecting Acanthamoeba, initiated a reappraisal of the upper limits of the viral world, both in terms of particle size (>0.7 micrometers) and genome complexity (>1000 genes), dimensions typical of parasitic bacteria. The diversity of these giant viruses (the Megaviridae) was assessed by sampling a variety of aquatic environments and their associated sediments worldwide. We report the isolation of two giant viruses, one off the coast of central Chile, the other from a freshwater pond near Melbourne (Australia), without morphological or genomic resemblance to any previously defined virus families. Their micrometer-sized ovoid particles contain DNA genomes of at least 2.5 and 1.9 megabases, respectively. These viruses are the first members of the proposed "Pandoravirus" genus, a term reflecting their lack of similarity with previously described microorganisms and the surprises expected from their future stud