22 results on '"Antoine Nougairède"'
Search Results
2. Comparison of chikungunya viruses generated using infectious clone or the Infectious Subgenomic Amplicons (ISA) method in Aedes mosquitoes.
- Author
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Souand Mohamed Ali, Anubis Vega-Rúa, Jean-Sélim Driouich, Xavier de Lamballerie, Anna-Bella Failloux, and Antoine Nougairède
- Subjects
Medicine ,Science - Abstract
Reverse genetics systems provide the opportunity to manipulate viral genomes and have been widely used to study RNA viruses and to develop new antiviral compounds and vaccine strategies. The recently described method called ISA (Infectious Subgenomic Amplicons) gives the possibility to rescue RNA viruses in days. We demonstrated in cell culture that the use of the ISA method led to a higher genetic diversity of viral populations than that observed using infectious clone technology. However, no replicative fitness difference was observed. In the present study, we used the chikungunya virus as a model to compare in Aedes aegypti and Aedes albopictus mosquitoes the genotypic and phenotypic characteristics of viruses produced either from an infectious clone or using the ISA method. We confirmed the results found in cellulo corroborating that the use of the ISA method was associated with higher genetic diversity of viral populations in mosquitoes but did not affect the vector competence validating its use for in vivo experiments.
- Published
- 2018
- Full Text
- View/download PDF
3. Haiku: New paradigm for the reverse genetics of emerging RNA viruses.
- Author
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Thérèse Atieh, Miriam Diala El Ayoubi, Fabien Aubry, Stéphane Priet, Xavier de Lamballerie, and Antoine Nougairède
- Subjects
Medicine ,Science - Abstract
Reverse genetics is key technology for producing wild-type and genetically modified viruses. The ISA (Infectious Subgenomic Amplicons) method is a recent versatile and user-friendly reverse genetics method to rescue RNA viruses. The main constraint of its canonic protocol was the requirement to produce (e.g., by DNA synthesis or fusion PCR) 5' and 3' modified genomic fragments encompassing the human cytomegalovirus promoter (pCMV) and the hepatitis delta virus ribozyme/simian virus 40 polyadenylation signal (HDR/SV40pA), respectively. Here, we propose the ultimately simplified "Haiku" designs in which terminal pCMV and HDR/SV40pA sequences are provided as additional separate DNA amplicons. This improved procedure was successfully applied to the rescue of a wide range of viruses belonging to genera Flavivirus, Alphavirus and Enterovirus in mosquito or mammalian cells using only standard PCR amplification techniques and starting from a variety of original materials including viral RNAs extracted from cell supernatant media or animal samples. We also demonstrate that, in specific experimental conditions, the presence of the HDR/SV40pA is not necessary to rescue the targeted viruses. These ultimately simplified "Haiku" designs provide an even more simple, rapid, versatile and cost-effective tool to rescue RNA viruses since only generation of overlapping amplicons encompassing the entire viral genome is now required to generate infectious virus. This new approach may completely modify our capacity to obtain infectious RNA viruses.
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- 2018
- Full Text
- View/download PDF
4. Utilisation of ISA Reverse Genetics and Large-Scale Random Codon Re-Encoding to Produce Attenuated Strains of Tick-Borne Encephalitis Virus within Days.
- Author
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Lauriane de Fabritus, Antoine Nougairède, Fabien Aubry, Ernest A Gould, and Xavier de Lamballerie
- Subjects
Medicine ,Science - Abstract
Large-scale codon re-encoding is a new method of attenuating RNA viruses. However, the use of infectious clones to generate attenuated viruses has inherent technical problems. We previously developed a bacterium-free reverse genetics protocol, designated ISA, and now combined it with large-scale random codon-re-encoding method to produce attenuated tick-borne encephalitis virus (TBEV), a pathogenic flavivirus which causes febrile illness and encephalitis in humans. We produced wild-type (WT) and two re-encoded TBEVs, containing 273 or 273+284 synonymous mutations in the NS5 and NS5+NS3 coding regions respectively. Both re-encoded viruses were attenuated when compared with WT virus using a laboratory mouse model and the relative level of attenuation increased with the degree of re-encoding. Moreover, all infected animals produced neutralizing antibodies. This novel, rapid and efficient approach to engineering attenuated viruses could potentially expedite the development of safe and effective new-generation live attenuated vaccines.
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- 2016
- Full Text
- View/download PDF
5. 'ISA-Lation' of Single-Stranded Positive-Sense RNA Viruses from Non-Infectious Clinical/Animal Samples.
- Author
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Fabien Aubry, Antoine Nougairède, Lauriane de Fabritus, Géraldine Piorkowski, Ernest A Gould, and Xavier de Lamballerie
- Subjects
Medicine ,Science - Abstract
Isolation of viral pathogens from clinical and/or animal samples has traditionally relied on either cell cultures or laboratory animal model systems. However, virus viability is notoriously susceptible to adverse conditions that may include inappropriate procedures for sample collection, storage temperature, support media and transportation. Using our recently described ISA method, we have developed a novel procedure to isolate infectious single-stranded positive-sense RNA viruses from clinical or animal samples. This approach, that we have now called "ISA-lation", exploits the capacity of viral cDNA subgenomic fragments to re-assemble and produce infectious viral RNA in susceptible cells. Here, it was successfully used to rescue enterovirus, Chikungunya and Tick-borne encephalitis viruses from a variety of inactivated animal and human samples. ISA-lation represents an effective option to rescue infectious virus from clinical and/or animal samples that may have deteriorated during the collection and storage period, but also potentially overcomes logistic and administrative difficulties generated when complying with current health and safety and biosecurity guidelines associated with shipment of infectious viral material.
- Published
- 2015
- Full Text
- View/download PDF
6. Molecular comparison and evolutionary analyses of VP1 nucleotide sequences of new African human enterovirus 71 isolates reveal a wide genetic diversity.
- Author
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Maël Bessaud, Richter Razafindratsimandresy, Antoine Nougairède, Marie-Line Joffret, Jagadish M Deshpande, Audrey Dubot-Pérès, Jean-Michel Héraud, Xavier de Lamballerie, Francis Delpeyroux, and Jean-Luc Bailly
- Subjects
Medicine ,Science - Abstract
Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied.
- Published
- 2014
- Full Text
- View/download PDF
7. Revolutionizing clinical microbiology laboratory organization in hospitals with in situ point-of-care.
- Author
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Stéphan Cohen-Bacrie, Laetitia Ninove, Antoine Nougairède, Rémi Charrel, Hervé Richet, Philippe Minodier, Sékéné Badiaga, Guilhem Noël, Bernard La Scola, Xavier de Lamballerie, Michel Drancourt, and Didier Raoult
- Subjects
Medicine ,Science - Abstract
BACKGROUND: Clinical microbiology may direct decisions regarding hospitalization, isolation and anti-infective therapy, but it is not effective at the time of early care. Point-of-care (POC) tests have been developed for this purpose. METHODS AND FINDINGS: One pilot POC-lab was located close to the core laboratory and emergency ward to test the proof of concept. A second POC-lab was located inside the emergency ward of a distant hospital without a microbiology laboratory. Twenty-three molecular and immuno-detection tests, which were technically undemanding, were progressively implemented, with results obtained in less than four hours. From 2008 to 2010, 51,179 tests yielded 6,244 diagnoses. The second POC-lab detected contagious pathogens in 982 patients who benefited from targeted isolation measures, including those undertaken during the influenza outbreak. POC tests prevented unnecessary treatment of patients with non-streptococcal tonsillitis (n = 1,844) and pregnant women negative for Streptococcus agalactiae carriage (n = 763). The cerebrospinal fluid culture remained sterile in 50% of the 49 patients with bacterial meningitis, therefore antibiotic treatment was guided by the molecular tests performed in the POC-labs. With regard to enterovirus meningitis, the mean length-of-stay of infected patients over 15 years old significantly decreased from 2008 to 2010 compared with 2005 when the POC was not in place (1.43±1.09 versus 2.91±2.31 days; p = 0.0009). Altogether, patients who received POC tests were immediately discharged nearly thrice as often as patients who underwent a conventional diagnostic procedure. CONCLUSIONS: The on-site POC-lab met physicians' needs and influenced the management of 8% of the patients that presented to emergency wards. This strategy might represent a major evolution of decision-making regarding the management of infectious diseases and patient care.
- Published
- 2011
- Full Text
- View/download PDF
8. Novel virus influenza A (H1N1sw) in South-Eastern France, April-August 2009.
- Author
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Antoine Nougairède, Laetitia Ninove, Christine Zandotti, Nicolas Salez, Karine Mantey, Noémie Resseguier, Céline Gazin, Didier Raoult, Rémi N Charrel, and Xavier de Lamballerie
- Subjects
Medicine ,Science - Abstract
BACKGROUND: In April 2009, the first cases of pandemic (H1N1)-2009 influenza [H1N1sw] virus were detected in France. Virological surveillance was undertaken in reference laboratories of the seven French Defence Zones. METHODOLOGY/PRINCIPAL FINDINGS: We report results of virological analyses performed in the Public Hospitals of Marseille during the first months of the outbreak. (i) Nasal swabs were tested using rapid influenza diagnostic test (RIDT) and two RT-PCR assays. Epidemiological characteristics of the 99 first suspected cases were analyzed, including detection of influenza virus and 18 other respiratory viruses. During three months, a total of 1,815 patients were tested (including 236 patients infected H1N1sw virus) and distribution in age groups and results of RIDT were analyzed. (ii) 600 sera received before April 2009 and randomly selected from in-patients were tested by a standard hemagglutination inhibition assay for antibody to the novel H1N1sw virus. (iii) One early (May 2009) and one late (July 2009) viral isolates were characterized by sequencing the complete hemagglutinine and neuraminidase genes. (iiii) Epidemiological characteristics of a cluster of cases that occurred in July 2009 in a summer camp were analyzed. CONCLUSIONS/SIGNIFICANCE: This study presents new virological and epidemiological data regarding infection by the pandemic A/H1N1 virus in Europe. Distribution in age groups was found to be similar to that previously reported for seasonal H1N1. The first seroprevalence data made available for a European population suggest a previous exposure of individuals over 40 years old to influenza viruses antigenically related to the pandemic (H1N1)-2009 virus. Genomic analysis indicates that strains harbouring a new amino-acid pattern in the neuraminidase gene appeared secondarily and tended to supplant the first strains. Finally, in contrast with previous reports, our data support the use of RIDT for the detection of infection in children, especially in the context of the investigation of grouped cases.
- Published
- 2010
- Full Text
- View/download PDF
9. Likely correlation between sources of information and acceptability of A/H1N1 swine-origin influenza virus vaccine in Marseille, France.
- Author
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Antoine Nougairède, Jean-Christophe Lagier, Laetitia Ninove, Catherine Sartor, Sékéné Badiaga, Elizabeth Botelho, Philippe Brouqui, Christine Zandotti, Xavier De Lamballerie, Bernard La Scola, Michel Drancourt, Ernest A Gould, Rémi N Charrel, and Didier Raoult
- Subjects
Medicine ,Science - Abstract
BACKGROUND: In France, there was a reluctance to accept vaccination against the A/H1N1 pandemic influenza virus despite government recommendation and investment in the vaccine programme. METHODS AND FINDINGS: We examined the willingness of different populations to accept A/H1N1 vaccination (i) in a French hospital among 3315 employees immunized either by in-house medical personnel or mobile teams of MDs and (ii) in a shelter housing 250 homeless persons. Google was used to assess the volume of enquiries concerning incidence of influenza. We analyzed the information on vaccination provided by Google, the website of the major French newspapers, and PubMed. Two trust Surveys were used to assess public opinion on the trustworthiness of people in different professions. Paramedics were significantly more reluctant to accept immunisation than qualified medical staff. Acceptance was significantly increased when recommended directly by MDs. Anecdotal cases of directly observed severe infections were followed by enhanced acceptance of paramedical staff. Scientific literature was significantly more in favour of vaccination than Google and French newspaper websites. In the case of the newspaper websites, information correlated with their recognised political reputations, although they would presumably claim independence from political bias. The Trust Surveys showed that politicians were highly dis-trusted in contrast with doctors and pharmacists who were considered much more trustworthy. CONCLUSIONS: The low uptake of the vaccine could reflect failure to convey high quality medical information and advice relating to the benefits of being vaccinated. We believe that the media and internet contributed to this problem by raising concerns within the general population and that failure to involve GPs in the control programme may have been a mistake. GPs are highly regarded by the public and can provide face-to-face professional advice and information. The top-down strategy of vaccine programme management and information delivered by the Ministry of Health could have aggravated the problem, because the general population does not always trust politicians.
- Published
- 2010
- Full Text
- View/download PDF
10. Niclosamide shows strong antiviral activity in a human airway model of SARS-CoV-2 infection and a conserved potency against the Alpha (B.1.1.7), Beta (B.1.351) and Delta variant (B.1.617.2)
- Author
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Xavier de Lamballerie, Magali Gilles, Bruno Hoen, Antoine Nougairède, Morten Otto Alexander Sommer, Cécile Baronti, Franck Touret, and Anne Weiss
- Subjects
RNA viruses ,Viral Diseases ,Coronaviruses ,Cytotoxicity ,Cell Lines ,Pharmacology ,Toxicology ,Epithelium ,Medical Conditions ,Chlorocebus aethiops ,Public and Occupational Health ,skin and connective tissue diseases ,Pathology and laboratory medicine ,Niclosamide ,Virus Testing ,Multidisciplinary ,Medical microbiology ,Vaccination and Immunization ,Infectious Diseases ,Viruses ,Medicine ,Biological Cultures ,SARS CoV 2 ,Pathogens ,Anatomy ,Research Article ,medicine.drug ,SARS coronavirus ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Science ,Immunology ,Alpha (ethology) ,Respiratory Mucosa ,Biology ,Research and Analysis Methods ,Microbiology ,Antiviral Agents ,Inhibitory Concentration 50 ,Antiviral Therapy ,Diagnostic Medicine ,Virology ,medicine ,Animals ,Humans ,Potency ,Beta (finance) ,Vero Cells ,Medicine and health sciences ,Biology and life sciences ,SARS-CoV-2 ,fungi ,Organisms ,Viral pathogens ,COVID-19 ,Covid 19 ,Human airway ,Viral Replication ,Microbial pathogens ,COVID-19 Drug Treatment ,respiratory tract diseases ,body regions ,Biological Tissue ,Caco-2 ,Preventive Medicine ,Caco-2 Cells - Abstract
SARS-CoV-2 variants are emerging with potential increased transmissibility highlighting the great unmet medical need for new therapies. Niclosamide is a potent anti-SARS-CoV-2 agent that has advanced in clinical development. We validate the potent antiviral efficacy of niclosamide in a SARS-CoV-2 human airway model. Furthermore, niclosamide remains its potency against the D614G, Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2) variants. Our data further support the potent anti-SARS-CoV-2 properties of niclosamide and highlights its great potential as a therapeutic agent for COVID-19.
- Published
- 2021
11. Comparison of chikungunya viruses generated using infectious clone or the Infectious Subgenomic Amplicons (ISA) method in Aedes mosquitoes
- Author
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Anna-Bella Failloux, Antoine Nougairède, Anubis Vega-Rúa, Xavier de Lamballerie, Souand Mohamed Ali, Jean-Sélim Driouich, Unité des Virus Emergents (UVE), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris], This work was supported by the French 'Agence Nationale de la Recherche' under grant agreement no. ANR-14-CE14-0001 (RNA Vacci-Code) and by the European Union's Horizon 2020 Research and Innovation Programme under grants agreements no. 653316 (European Virus Archive goes global project: https://www.european-virus-archive.com/)., ANR-14-CE14-0001,RNA Vacci-Code,Ré-encodage génomique à large échelle des virus ARN pour la production de candidats vaccins atténués(2014), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut Pasteur [Paris] (IP)
- Subjects
0301 basic medicine ,RNA viruses ,Viral Diseases ,viruses ,lcsh:Medicine ,Disease Vectors ,medicine.disease_cause ,Pathology and Laboratory Medicine ,Mosquitoes ,Aedes ,Chlorocebus aethiops ,Medicine and Health Sciences ,Chikungunya ,lcsh:Science ,Subgenomic mRNA ,Multidisciplinary ,Chikungunya Virus ,Microbial Genetics ,Eukaryota ,Biological Evolution ,3. Good health ,Insects ,Infectious Diseases ,Medical Microbiology ,Viral Pathogens ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Viruses ,RNA, Viral ,Female ,Pathogens ,Research Article ,Neglected Tropical Diseases ,Aedes albopictus ,Substitution Mutation ,Arthropoda ,Alphaviruses ,Aedes aegypti ,Genome, Viral ,Biology ,Aedes Aegypti ,Research and Analysis Methods ,Microbiology ,Virus ,Togaviruses ,03 medical and health sciences ,medicine ,Genetics ,Animals ,Molecular Biology Techniques ,Microbial Pathogens ,Molecular Biology ,Vero Cells ,Evolutionary Biology ,Population Biology ,lcsh:R ,Organisms ,Biology and Life Sciences ,Chikungunya Infection ,Genetic Variation ,biology.organism_classification ,Tropical Diseases ,Virology ,Invertebrates ,Reverse genetics ,Insect Vectors ,Species Interactions ,030104 developmental biology ,Vector (epidemiology) ,Mutation ,lcsh:Q ,Population Genetics ,Cloning - Abstract
International audience; Reverse genetics systems provide the opportunity to manipulate viral genomes and have been widely used to study RNA viruses and to develop new antiviral compounds and vaccine strategies. The recently described method called ISA (Infectious Subgenomic Amplicons) gives the possibility to rescue RNA viruses in days. We demonstrated in cell culture that the use of the ISA method led to a higher genetic diversity of viral populations than that observed using infectious clone technology. However, no replicative fitness difference was observed. In the present study, we used the chikungunya virus as a model to compare in Aedes aegypti and Aedes albopictus mosquitoes the genotypic and phenotypic characteristics of viruses produced either from an infectious clone or using the ISA method. We confirmed the results found in cellulo corroborating that the use of the ISA method was associated with higher genetic diversity of viral populations in mosquitoes but did not affect the vector competence validating its use for in vivo experiments.
- Published
- 2018
12. A retrospective overview of enterovirus infection diagnosis and molecular epidemiology in the public hospitals of Marseille, France (1985-2005)
- Author
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Xavier de Lamballerie, Rémi N. Charrel, Antoine Nougairède, Jean Gaudart, Christine Zandotti, Charlene Y. Q. Tan, Laurence Thirion-Perrier, and Laetitia Ninove
- Subjects
Serotype ,Viral Diseases ,Echovirus ,Epidemiology ,viruses ,medicine.disease_cause ,Emerging Viral Diseases ,Phylogeny ,Enterovirus ,Recombination, Genetic ,Molecular Epidemiology ,Multidisciplinary ,Phylogenetic tree ,Reverse Transcriptase Polymerase Chain Reaction ,Aseptic meningitis ,virus diseases ,Phylogenetics ,Infectious Diseases ,Medical Microbiology ,Medicine ,France ,Research Article ,Clinical Research Design ,Science ,Biology ,Coxsackievirus ,Microbiology ,Viral Evolution ,Cell Line ,Evolution, Molecular ,Neutralization Tests ,Virology ,Enterovirus Infections ,medicine ,Animals ,Humans ,Evolutionary Systematics ,Serotyping ,Retrospective Studies ,Evolutionary Biology ,Molecular epidemiology ,Hospitals, Public ,Computational Biology ,Outbreak ,medicine.disease ,biology.organism_classification ,Viral Disease Diagnosis ,Viral Classification ,Emerging Infectious Diseases ,Enterovirus Infection ,Population Genetics - Abstract
Human enteroviruses (HEV) are frequent human pathogens and, associated in particular with large outbreaks of aseptic meningitis. Here, we have compiled a database of clinical HEV isolates from the Public Hospitals of Marseille, from 1985 to 2005. Amongst 654 isolates that could be characterized by complete sequencing of the VP1 gene, 98% belonged to species HEV-B; the most frequently isolated serotypes were Echovirus E30, E11, E7, E6 and E4. The high incidence of E30 and the recent emergence of E13 are consistent with reports worldwide and peak HEV isolation occurred mostly in the late spring and summer months. The proportion of echoviruses has decreased across the years, while that of coxsackieviruses has increased. Stool (the most frequent sample type) allowed detection of all identified serotypes. MRC5 (Human lung fibroblasts) cell line was the most conducive cell line for HEV isolation (84.9% of 10 most common serotype isolates, 96.3% in association with BGM (Buffalo green monkey kidney cells)). Previous seroneutralization-based serotype identification demonstrated 55.4% accuracy when compared with molecular VP1 analysis. Our analysis of a large number of clinical strains over 20 years reinforced the validity of VP1 serotyping and showed that comparative p-distance scores can be coupled with phylogenetic analysis to provide non-ambiguous serotype identification. Phylogenetic analysis in the VP1, 2C and 3D regions also provided evidence for recombination events amongst clinical isolates. In particular, it identified isolates with dissimilar VP1 but almost identical nonstructural regions.
- Published
- 2011
13. Revolutionizing clinical microbiology laboratory organization in hospitals with in situ point-of-care
- Author
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Guilhem Noel, Michel Drancourt, Sékéné Badiaga, Philippe Minodier, Antoine Nougairède, Rémi N. Charrel, Didier Raoult, Stéphan Cohen-Bacrie, Laetitia Ninove, Hervé Richet, Bernard La Scola, and Xavier de Lamballerie
- Subjects
medicine.medical_specialty ,Enterovirus Infections ,Critical Care and Emergency Medicine ,Clinical Pathology ,Isolation (health care) ,Non-Clinical Medicine ,Point-of-Care Systems ,MEDLINE ,lcsh:Medicine ,Microbiology ,Diagnostic Medicine ,Pathology ,Medicine ,Humans ,Intensive care medicine ,lcsh:Science ,Biology ,Point of care ,Multidisciplinary ,business.industry ,Clinical Laboratory Techniques ,lcsh:R ,Length of Stay ,Laboratories, Hospital ,Patient Care Management ,Hospitalization ,Clinical microbiology ,Clinical Microbiology ,Kinetics ,Infectious Diseases ,Female ,lcsh:Q ,Health Services Research ,business ,Research Article - Abstract
BACKGROUND: Clinical microbiology may direct decisions regarding hospitalization, isolation and anti-infective therapy, but it is not effective at the time of early care. Point-of-care (POC) tests have been developed for this purpose. METHODS AND FINDINGS: One pilot POC-lab was located close to the core laboratory and emergency ward to test the proof of concept. A second POC-lab was located inside the emergency ward of a distant hospital without a microbiology laboratory. Twenty-three molecular and immuno-detection tests, which were technically undemanding, were progressively implemented, with results obtained in less than four hours. From 2008 to 2010, 51,179 tests yielded 6,244 diagnoses. The second POC-lab detected contagious pathogens in 982 patients who benefited from targeted isolation measures, including those undertaken during the influenza outbreak. POC tests prevented unnecessary treatment of patients with non-streptococcal tonsillitis (n = 1,844) and pregnant women negative for Streptococcus agalactiae carriage (n = 763). The cerebrospinal fluid culture remained sterile in 50% of the 49 patients with bacterial meningitis, therefore antibiotic treatment was guided by the molecular tests performed in the POC-labs. With regard to enterovirus meningitis, the mean length-of-stay of infected patients over 15 years old significantly decreased from 2008 to 2010 compared with 2005 when the POC was not in place (1.43±1.09 versus 2.91±2.31 days; p = 0.0009). Altogether, patients who received POC tests were immediately discharged nearly thrice as often as patients who underwent a conventional diagnostic procedure. CONCLUSIONS: The on-site POC-lab met physicians' needs and influenced the management of 8% of the patients that presented to emergency wards. This strategy might represent a major evolution of decision-making regarding the management of infectious diseases and patient care.
- Published
- 2011
14. Point of Care Strategy for Rapid Diagnosis of Novel A/H1N1 Influenza Virus
- Author
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Antoine Nougairède, Xavier de Lamballerie, Christine Zandotti, Didier Raoult, Bernard La Scola, Michel Drancourt, Celine Gazin, Rémi N. Charrel, and Laetitia Ninove
- Subjects
medicine.medical_specialty ,Multidisciplinary ,business.industry ,Statement (logic) ,Science ,lcsh:R ,Alternative medicine ,lcsh:Medicine ,Correction ,Family medicine ,A h1n1 influenza ,Agency (sociology) ,medicine ,Medicine ,lcsh:Q ,business ,lcsh:Science ,Point of care - Abstract
The following information was omitted from the funding statement: This study has been partly funded by (i) the PHRC 2008-A00793-52, (ii) the PhleboMED project #ANR-08-MIE-023 (National Research Agency).
- Published
- 2010
15. Likely correlation between sources of information and acceptability of A/H1N1 swine-origin influenza virus vaccine in Marseille, France
- Author
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Didier Raoult, Michel Drancourt, Antoine Nougairède, Bernard La Scola, Philippe Brouqui, Rémi N. Charrel, Sékéné Badiaga, Xavier de Lamballerie, C. Sartor, Jean-Christophe Lagier, Christine Zandotti, Ernest A. Gould, Laetitia Ninove, and Elizabeth Botelho
- Subjects
medicine.medical_specialty ,Population ,Public Health and Epidemiology/Infectious Diseases ,lcsh:Medicine ,Mistake ,Scientific literature ,Public opinion ,Virology/Emerging Viral Diseases ,Newspaper ,Public Health and Epidemiology/Immunization ,Politics ,Influenza A Virus, H1N1 Subtype ,Medicine ,Humans ,education ,lcsh:Science ,Public Health and Epidemiology/Occupational and Industrial Medicine ,Government ,education.field_of_study ,Multidisciplinary ,business.industry ,Data Collection ,lcsh:R ,Microbiology/Medical Microbiology ,Patient Acceptance of Health Care ,Vaccination ,Influenza Vaccines ,Family medicine ,Public Opinion ,Immunology ,Ill-Housed Persons ,lcsh:Q ,France ,business ,Research Article - Abstract
BACKGROUND: In France, there was a reluctance to accept vaccination against the A/H1N1 pandemic influenza virus despite government recommendation and investment in the vaccine programme. METHODS AND FINDINGS: We examined the willingness of different populations to accept A/H1N1 vaccination (i) in a French hospital among 3315 employees immunized either by in-house medical personnel or mobile teams of MDs and (ii) in a shelter housing 250 homeless persons. Google was used to assess the volume of enquiries concerning incidence of influenza. We analyzed the information on vaccination provided by Google, the website of the major French newspapers, and PubMed. Two trust Surveys were used to assess public opinion on the trustworthiness of people in different professions. Paramedics were significantly more reluctant to accept immunisation than qualified medical staff. Acceptance was significantly increased when recommended directly by MDs. Anecdotal cases of directly observed severe infections were followed by enhanced acceptance of paramedical staff. Scientific literature was significantly more in favour of vaccination than Google and French newspaper websites. In the case of the newspaper websites, information correlated with their recognised political reputations, although they would presumably claim independence from political bias. The Trust Surveys showed that politicians were highly dis-trusted in contrast with doctors and pharmacists who were considered much more trustworthy. CONCLUSIONS: The low uptake of the vaccine could reflect failure to convey high quality medical information and advice relating to the benefits of being vaccinated. We believe that the media and internet contributed to this problem by raising concerns within the general population and that failure to involve GPs in the control programme may have been a mistake. GPs are highly regarded by the public and can provide face-to-face professional advice and information. The top-down strategy of vaccine programme management and information delivered by the Ministry of Health could have aggravated the problem, because the general population does not always trust politicians.
- Published
- 2010
16. Point of care strategy for rapid diagnosis of novel A/H1N1 influenza virus
- Author
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Michel Drancourt, Didier Raoult, Xavier de Lamballerie, Rémi N. Charrel, Christine Zandotti, Bernard La Scola, Antoine Nougairède, Celine Gazin, and Laetitia Ninove
- Subjects
Infectious Diseases/Epidemiology and Control of Infectious Diseases ,Pediatrics ,medicine.medical_specialty ,Point-of-Care Systems ,lcsh:Medicine ,Medicine (miscellaneous) ,medicine.disease_cause ,Sensitivity and Specificity ,Virus ,Disease Outbreaks ,03 medical and health sciences ,0302 clinical medicine ,Influenza A Virus, H1N1 Subtype ,Infectious Diseases/Viral Infections ,Pandemic ,A h1n1 influenza ,Epidemiology ,Influenza, Human ,medicine ,Influenza A virus ,Humans ,030212 general & internal medicine ,lcsh:Science ,Point of care ,0303 health sciences ,Multidisciplinary ,030306 microbiology ,business.industry ,Hospitals, Public ,Reverse Transcriptase Polymerase Chain Reaction ,Infectious Diseases/Respiratory Infections ,lcsh:R ,H1N1 influenza ,Virology/Diagnosis ,medicine.disease ,Virology ,Influenza A virus subtype H5N1 ,3. Good health ,H1n1 pandemic ,Emergency medicine ,lcsh:Q ,Medical emergency ,France ,business ,Research Article - Abstract
Background Within months of the emergence of the novel A/H1N1 pandemic influenza virus (nA/H1N1v), systematic screening for the surveillance of the pandemic was abandoned in France and in some other countries. At the end of June 2009, we implemented, for the public hospitals of Marseille, a Point Of Care (POC) strategy for rapid diagnosis of the novel A/H1N1 influenza virus, in order to maintain local surveillance and to evaluate locally the kinetics of the pandemic. Methodology/Principal Findings Two POC laboratories, located in strategic places, were organized to receive and test samples 24 h/24. POC strategy consisted of receiving and processing naso-pharyngeal specimens in preparation for the rapid influenza diagnostic test (RIDT) and real-time RT-PCR assay (rtRT-PCR). This strategy had the theoretical capacity of processing up to 36 samples per 24 h. When the flow of samples was too high, the rtRT-PCR test was abandoned in the POC laboratories and transferred to the core virology laboratory. Confirmatory diagnosis was performed in the core virology laboratory twice a day using two distinct rtRT-PCR techniques that detect either influenza A virus or nA/N1N1v. Over a period of three months, 1974 samples were received in the POC laboratories, of which 111 were positive for nA/H1N1v. Specificity and sensitivity of RIDT were 100%, and 57.7% respectively. Positive results obtained using RIDT were transmitted to clinical practitioners in less than 2 hours. POC processed rtRT-PCR results were available within 7 hours, and rtRT-PCR confirmation within 24 hours. Conclusions/Significance The POC strategy is of benefit, in all cases (with or without rtRT-PCR assay), because it provides continuous reception/processing of samples and reduction of the time to provide consolidated results to the clinical practitioners. We believe that implementation of the POC strategy for the largest number of suspect cases may improve the quality of patient care and our knowledge of the epidemiology of the pandemic.
- Published
- 2009
17. New Insights into Flavivirus Evolution, Taxonomy and Biogeographic History, Extended by Analysis of Canonical and Alternative Coding Sequences
- Author
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Ernest A. Gould, Xavier de Lamballerie, Philippe Lemey, Antoine Nougairède, Shelley Cook, Rémi N. Charrel, Gregory Moureau, Naomi L. Forrester, Khasnatinov Ma, Andrew E. Firth, Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Life Sciences, The Natural History Museum [London] (NHM), Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Institute for Human Infections and Immunity and Department of Pathology, The University of Texas Medical Branch (UTMB), Centre for Ecology and Hydrology, Maclean Building, Division of Virology, University of Cambridge [UK] (CAM), and Lee, Young-Min
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BAGAZA VIRUS ,Old World ,Science ,viruses ,Molecular Sequence Data ,GENUS FLAVIVIRUS ,Genomics ,Genome, Viral ,INSECT-SPECIFIC FLAVIVIRUSES ,Biology ,Q1 ,WEST-NILE-VIRUS ,complex mixtures ,Genome ,Evolution, Molecular ,Open Reading Frames ,Phylogenetics ,NATURAL MOSQUITO POPULATION ,DENGUE VIRUS ,Phylogeny ,Genetics ,Translational frameshift ,Multidisciplinary ,Base Sequence ,Phylogenetic tree ,Flavivirus ,Frameshifting, Ribosomal ,virus diseases ,NORTH-AMERICA ,FUSING AGENT VIRUS ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,ENCEPHALITIS-VIRUS ,Phylogeography ,Biology and Microbiology ,TICK-BORNE FLAVIVIRUSES ,Evolutionary biology ,Viral evolution ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Medicine ,Research Article - Abstract
To generate the most diverse phylogenetic dataset for the flaviviruses to date, we determined the genomic sequences and phylogenetic relationships of 14 flaviviruses, of which 10 are primarily associated with Culex spp. mosquitoes. We analyze these data, in conjunction with a comprehensive collection of flavivirus genomes, to characterize flavivirus evolutionary and biogeographic history in unprecedented detail and breadth. Based on the presumed introduction of yellow fever virus into the Americas via the transatlantic slave trade, we extrapolated a timescale for a relevant subset of flaviviruses whose evolutionary history, shows that different Culex-spp. associated flaviviruses have been introduced from the Old World to the New World on at least five separate occasions, with 2 different sets of factors likely to have contributed to the dispersal of the different viruses. We also discuss the significance of programmed ribosomal frameshifting in a central region of the polyprotein open reading frame in some mosquito-associated flaviviruses. ispartof: PLoS One vol:10 issue:2 ispartof: location:United States status: published
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- 2015
18. New insights into flavivirus evolution, taxonomy and biogeographic history, extended by analysis of canonical and alternative coding sequences.
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Gregory Moureau, Shelley Cook, Philippe Lemey, Antoine Nougairede, Naomi L Forrester, Maxim Khasnatinov, Remi N Charrel, Andrew E Firth, Ernest A Gould, and Xavier de Lamballerie
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Medicine ,Science - Abstract
To generate the most diverse phylogenetic dataset for the flaviviruses to date, we determined the genomic sequences and phylogenetic relationships of 14 flaviviruses, of which 10 are primarily associated with Culex spp. mosquitoes. We analyze these data, in conjunction with a comprehensive collection of flavivirus genomes, to characterize flavivirus evolutionary and biogeographic history in unprecedented detail and breadth. Based on the presumed introduction of yellow fever virus into the Americas via the transatlantic slave trade, we extrapolated a timescale for a relevant subset of flaviviruses whose evolutionary history, shows that different Culex-spp. associated flaviviruses have been introduced from the Old World to the New World on at least five separate occasions, with 2 different sets of factors likely to have contributed to the dispersal of the different viruses. We also discuss the significance of programmed ribosomal frameshifting in a central region of the polyprotein open reading frame in some mosquito-associated flaviviruses.
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- 2015
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19. First reported chikungunya fever outbreak in the republic of Congo, 2011.
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Nanikaly Moyen, Simon-Djamel Thiberville, Boris Pastorino, Antoine Nougairede, Laurence Thirion, Jean-Vivien Mombouli, Yannick Dimi, Isabelle Leparc-Goffart, Maria Rosaria Capobianchi, Amelia Dzia Lepfoundzou, and Xavier de Lamballerie
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Medicine ,Science - Abstract
Chikungunya is an Aedes -borne disease characterised by febrile arthralgia and responsible for massive outbreaks. We present a prospective clinical cohort study and a retrospective serological study relating to a CHIK outbreak, in the Republic of Congo in 2011.We analysed 317 suspected cases, of which 308 (97.2%) lived in the city of Brazzaville (66.6% in the South area). Amongst them, 37 (11.7%) were CHIKV+ve patients (i.e., biologically confirmed by a real-time RT-PCR assay), of whom 36 (97.3%) had fever, 22 (66.7%) myalgia and 32 (86.5%) arthralgia. All tested negative for dengue. The distribution of incident cases within Brazzaville districts was compared with CHIKV seroprevalence before the outbreak (34.4% in 517 blood donors), providing evidence for previous circulation of CHIKV. We applied a CHIK clinical score to 126 patients recruited within the two first day of illness (including 28 CHIKV+ves (22.2%)) with sensitivity (78.6%) and specificity (72.4%) values comparing with those of the referent study in Reunion Island. The negative predictive value was high (92%), but the positive predictive value (45%) indicate poor potential contribution to medical practice to identify CHIKV+ve patients in low prevalence outbreaks. However, the score allowed a slightly more accurate follow-up of the evolution of the outbreak than the criterion "fever+arthralgia". The complete sequencing of a Congolase isolate (Brazza_MRS1) demonstrated belonging to the East/Central/South African lineage and was further used for producing a robust genome-scale CHIKV phylogenetic analysis.We describe the first Chikungunya outbreak declared in the Republic of Congo. The seroprevalence study conducted amongst blood donors before outbreak provided evidence for previous CHIKV circulation. We suggest that a more systematic survey of the entomological situation and of arbovirus circulation is necessary in Central Africa for better understanding the environmental, microbiological and sociological determinants of emergence.
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- 2014
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20. A retrospective overview of enterovirus infection diagnosis and molecular epidemiology in the public hospitals of Marseille, France (1985-2005).
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Charlene Y Q Tan, Laetitia Ninove, Jean Gaudart, Antoine Nougairede, Christine Zandotti, Laurence Thirion-Perrier, Remi N Charrel, and Xavier de Lamballerie
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Medicine ,Science - Abstract
Human enteroviruses (HEV) are frequent human pathogens and, associated in particular with large outbreaks of aseptic meningitis. Here, we have compiled a database of clinical HEV isolates from the Public Hospitals of Marseille, from 1985 to 2005. Amongst 654 isolates that could be characterized by complete sequencing of the VP1 gene, 98% belonged to species HEV-B; the most frequently isolated serotypes were Echovirus E30, E11, E7, E6 and E4. The high incidence of E30 and the recent emergence of E13 are consistent with reports worldwide and peak HEV isolation occurred mostly in the late spring and summer months. The proportion of echoviruses has decreased across the years, while that of coxsackieviruses has increased. Stool (the most frequent sample type) allowed detection of all identified serotypes. MRC5 (Human lung fibroblasts) cell line was the most conducive cell line for HEV isolation (84.9% of 10 most common serotype isolates, 96.3% in association with BGM (Buffalo green monkey kidney cells)). Previous seroneutralization-based serotype identification demonstrated 55.4% accuracy when compared with molecular VP1 analysis. Our analysis of a large number of clinical strains over 20 years reinforced the validity of VP1 serotyping and showed that comparative p-distance scores can be coupled with phylogenetic analysis to provide non-ambiguous serotype identification. Phylogenetic analysis in the VP1, 2C and 3D regions also provided evidence for recombination events amongst clinical isolates. In particular, it identified isolates with dissimilar VP1 but almost identical nonstructural regions.
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- 2011
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21. RNA and DNA bacteriophages as molecular diagnosis controls in clinical virology: a comprehensive study of more than 45,000 routine PCR tests.
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Laetitia Ninove, Antoine Nougairede, Celine Gazin, Laurence Thirion, Ilenia Delogu, Christine Zandotti, Remi N Charrel, and Xavier De Lamballerie
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Medicine ,Science - Abstract
Real-time PCR techniques are now commonly used for the detection of viral genomes in various human specimens and require for validation both external and internal controls (ECs and ICs). In particular, ICs added to clinical samples are necessary to monitor the extraction, reverse transcription, and amplification steps in order to detect false-negative results resulting from PCR-inhibition or errors in the technical procedure. Here, we performed a large scale evaluation of the use of bacteriophages as ICs in routine molecular diagnosis. This allowed to propose simple standardized procedures (i) to design specific ECs for both DNA and RNA viruses and (ii) to use T4 (DNA) or MS2 (RNA) phages as ICs in routine diagnosis. Various technical formats for using phages as ICs were optimised and validated. Subsequently, T4 and MS2 ICs were evaluated in routine real-time PCR or RT-PCR virological diagnostic tests, using a series of 8,950 clinical samples (representing 36 distinct specimen types) sent to our laboratory for the detection of a variety of DNA and RNA viruses. The frequency of inefficient detection of ICs was analyzed according to the nature of the sample. Inhibitors of enzymatic reactions were detected at high frequency in specific sample types such as heparinized blood and bone marrow (>70%), broncho-alveolar liquid (41%) and stools (36%). The use of T4 and MS2 phages as ICs proved to be cost-effective, flexible and adaptable to various technical procedures of real-time PCR detection in virology. It represents a valuable strategy for enhancing the quality of routine molecular diagnosis in laboratories that use in-house designed diagnostic systems, which can conveniently be associated to the use of specific synthetic ECs. The high rate of inhibitors observed in a variety of specimen types should stimulate the elaboration of improved technical protocols for the extraction and amplification of nucleic acids.
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- 2011
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22. Correction: Point of Care Strategy for Rapid Diagnosis of Novel A/H1N1 Influenza Virus.
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Antoine Nougairede, Laetitia Ninove, Christine Zandotti, Xavier de Lamballerie, Celine Gazin, Michel Drancourt, Bernard La Scola, Didier Raoult, and Remi N. Charrel
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Medicine ,Science - Published
- 2010
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