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1. EFFECTIVENESS OF EXOGENOUS DIGESTIVE ENZYMES SUPPLEMENTATION ON THE PERFORMANCE OF RABBITFISH (Siganus rivulatus)

Author: Elsaid Abdelraouf, Eman M. Moustafa, Mohamed Mohsen, Hamada A. Ahmed, Ashraf Y. El-Dakar, and Mahmoud A.O. Dawood
Subjects: chemistry.chemical_classification, 0303 health sciences, General Veterinary, medicine.diagnostic_test, Globulin, biology, Physiological condition, Soybean meal, 04 agricultural and veterinary sciences, Hematocrit, biology.organism_classification, Feed conversion ratio, Siganus rivulatus, 03 medical and health sciences, Enzyme, Animal science, chemistry, 040102 fisheries, medicine, biology.protein, 0401 agriculture, forestry, and fisheries, Rabbitfish, 030304 developmental biology
Abstract: The current study was established to test the possibility of using exogenous digestive enzymes (EDE) in rabbitfish ( Siganus rivulatus ) diets . Five experimental diets containing 34% soybean meal were prepared and supplemented with EDE at 0, 1, 2, 3, and 4 g kg -1 diet. Fish with average initial weight (Â± 1.1 g) were fed the test diets for 74 days. Rabbitfish offered the diets with EDE supplements exhibited significantly ( P 0.05) differences were observed in carcass composition and somatic parameters index with EDE supplementation. The physiological condition of fish fed diets with EDE showed that the hematocrit (%), total plasma protein and total plasma globulin were significantly ( P
Published: 2019
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2. Evaluation of Time to Fracture and Vertical Forces Applied by a Novel Gentlefile System for Root Canal Preparation in Simulated Root Canals

Author: Daniel Moreinos, Nachum Joseph Stone, Joshua Moshonov, and Aharon Dakar
Subjects: 0301 basic medicine, Cyclic stress, Dental Instruments, Root canal, Root (chord), Tooth Fracture, 03 medical and health sciences, Tooth Fractures, 0302 clinical medicine, Nickel, Materials Testing, medicine, Humans, General Dentistry, Mathematics, Titanium, Dental alloys, business.industry, Metallurgy, 030206 dentistry, Structural engineering, Equipment Design, Stainless Steel, Dental instruments, Root Canal Therapy, 030104 developmental biology, medicine.anatomical_structure, Nickel titanium, Fracture (geology), Equipment Failure, Dental Pulp Cavity, business, Root Canal Preparation, Dental Alloys
Abstract: A great number of studies performed in the last 3 decades have shown the superior mechanical features of nickel-titanium files as compared with stainless steel files. A novel file system recently developed, Gentlefile, defies these findings and claims to have superior qualities despite the fact it is made from stainless steel.Three file systems were used in this experiment: ProTaper Next (X1, X2, and X3), RevoS (SC2, SC3, and AS30), and Gentlefile (GF1, GF2, and GF3). Time to fracture, rotations to fracture, and vertical forces applied to a simulated root canal, which was fabricated from a metal block with a Plexiglas cover, were measured.The GF system required significantly longer time and more rotations to fracture compared with the ProTaper and RevoS systems (P .001). The GF system applied significantly less vertical force to the canal in comparison with the ProTaper and RevoS systems (P .01).Under the limitations of this study the GF system showed better mechanical properties in comparison with the ProTaper and RevoS systems. Further investigation is needed to assess the clinical meaning of these findings.
Published: 2015

3. Three Main Mutational Pathways in HIV-2 Lead to High-Level Raltegravir and Elvitegravir Resistance: Implications for Emerging HIV-2 Treatment Regimens

Author: Robert A Smith, Dana N Raugi, Charlotte Pan, Matthew Coyne, Alexandra Hernandez, Brad Church, Kara Parker, James I Mullins, Papa Salif Sow, Geoffrey S Gottlieb, and University of Washington-Dakar HIV-2 Study Group
Subjects: Integrase inhibitor, lcsh:Medicine, Drug resistance, Quinolones, Virus Replication, Biochemistry, Raltegravir Potassium, 0302 clinical medicine, Immunodeficiency Viruses, Drug Discovery, 030212 general & internal medicine, lcsh:Science, Genetics, 0303 health sciences, Multidisciplinary, Elvitegravir, HIV diagnosis and management, Antivirals, Pyrrolidinones, 3. Good health, Integrase, AIDS, Viral Enzymes, Medicine, Infectious diseases, medicine.drug, Research Article, Biotechnology, Signal Transduction, Drugs and Devices, Drug Research and Development, Mechanisms of Resistance and Susceptibility, Sexually Transmitted Diseases, Viral diseases, Biology, Microbiology, Cell Line, 03 medical and health sciences, Virology, Drug Resistance, Viral, medicine, Humans, HIV Integrase Inhibitors, 030306 microbiology, lcsh:R, HIV, Raltegravir, Reverse transcriptase, Viral replication, HIV-2, Mutation, biology.protein, lcsh:Q
Abstract: Human immunodeficiency virus type 2 (HIV-2) is intrinsically resistant to non-nucleoside reverse transcriptase inhibitors and exhibits reduced susceptibility to several of the protease inhibitors used for antiretroviral therapy of HIV-1. Thus, there is a pressing need to identify new classes of antiretroviral agents that are active against HIV-2. Although recent data suggest that the integrase strand transfer inhibitors raltegravir and elvitegravir may be beneficial, mutations that are known to confer resistance to these drugs in HIV-1 have been reported in HIV-2 sequences from patients receiving raltegravir-containing regimens. To examine the phenotypic effects of mutations that emerge during raltegravir treatment, we constructed a panel of HIV-2 integrase variants using site-directed mutagenesis and measured the susceptibilities of the mutant strains to raltegravir and elvitegravir in culture. The effects of single and multiple amino acid changes on HIV-2 replication capacity were also evaluated. Our results demonstrate that secondary replacements in the integrase protein play key roles in the development of integrase inhibitor resistance in HIV-2. Collectively, our data define three major mutational pathways to high-level raltegravir and elvitegravir resistance: i) E92Q+Y143C or T97A+Y143C, ii) G140S+Q148R, and iii) E92Q+N155H. These findings preclude the sequential use of raltegravir and elvitegravir (or vice versa) for HIV-2 treatment and provide important information for clinical monitoring of integrase inhibitor resistance in HIV-2–infected individuals.
Published: 2012

4. HIV-2 Integrase Variation in Integrase Inhibitor-Naïve Adults in Senegal, West Africa

Author: Geoffrey S Gottlieb, Robert A Smith, Ndeye Mery Dia Badiane, Selly Ba, Stephen E Hawes, Macoumba Toure, Alison K Starling, Fatou Traore, Fatima Sall, Stephen L Cherne, Joshua Stern, Kim G Wong, Paul Lu, Moon Kim, Dana N Raugi, Airin Lam, James I Mullins, Nancy B Kiviat, and Papa Salif Sow for the UW-Dakar HIV-2 Study Group
Subjects: Male, lcsh:Medicine, Integrase inhibitor, HIV Integrase, Drug resistance, 0302 clinical medicine, Genotype, 030212 general & internal medicine, lcsh:Science, Phylogeny, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, Elvitegravir, virus diseases, HIV diagnosis and management, Middle Aged, Senegal, 3. Good health, Integrase, AIDS, Medicine, Infectious diseases, Female, Research Article, medicine.drug, Adult, Molecular Sequence Data, Population, Sexually Transmitted Diseases, Retrovirology and HIV immunopathogenesis, Viral diseases, Biology, Microbiology, Young Adult, 03 medical and health sciences, Virology, Drug Resistance, Viral, Retroviruses, Genetic variation, medicine, Humans, HIV Integrase Inhibitors, education, Base Sequence, 030306 microbiology, lcsh:R, Genetic Variation, HIV, Raltegravir, Viral Classification, HIV-2, biology.protein, lcsh:Q
Abstract: Background Antiretroviral therapy for HIV-2 infection is hampered by intrinsic resistance to many of the drugs used to treat HIV-1. Limited studies suggest that the integrase inhibitors (INIs) raltegravir and elvitegravir have potent activity against HIV-2 in culture and in infected patients. There is a paucity of data on genotypic variation in HIV-2 integrase that might confer intrinsic or transmitted INI resistance. Methods We PCR amplified and analyzed 122 HIV-2 integrase consensus sequences from 39 HIV-2–infected, INI-naive adults in Senegal, West Africa. We assessed genetic variation and canonical mutations known to confer INI-resistance in HIV-1. Results No amino acid-altering mutations were detected at sites known to be pivotal for INI resistance in HIV-1 (integrase positions 143, 148 and 155). Polymorphisms at several other HIV-1 INI resistance-associated sites were detected at positions 72, 95, 125, 154, 165, 201, 203, and 263 of the HIV-2 integrase protein. Conclusion Emerging genotypic and phenotypic data suggest that HIV-2 is susceptible to the new class of HIV integrase inhibitors. We hypothesize that intrinsic HIV-2 integrase variation at “secondary” HIV-1 INI-resistance sites may affect the genetic barrier to HIV-2 INI resistance. Further studies will be needed to assess INI efficacy as part of combination antiretroviral therapy in HIV-2–infected patients.
Published: 2011
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5. Hepatitis B in Senegal: A Successful Infant Vaccination Program but Urgent Need to Scale Up Screening and Treatment (ANRS 12356 AmBASS survey)

Author: Périères, Lauren, Diallo, Aldiouma, Marcellin, Fabienne, Nishimwe, Marie Libérée, Ba, El Hadji, Coste, Marion, Lo, Gora, Halfon, Philippe, Touré Kane, Coumba, Maradan, Gwenaëlle, Carrieri, Patrizia, Diouf, Assane, Shimakawa, Yusuke, Sokhna, Cheikh, Boyer, Sylvie, Bérenger, Cyril, Bousmah, Marwan al Qays, de Seze, Maëlle, Djaogol, Tchadine, Treibich, Carole, Ba, Elhadji, Dièye, Fambaye, Faye, Elhadji Bilal, Ndiaye, Assane, Sow, Mouhamadou Baba, Ndiaye, Anna Julienne Selbé, Ndiour, Samba, Mohamed, Sofiane, Rouveau, Nicolas, Cortès, Maria‐Camila Calvo, Laborde‐Balen, Gabrièle, Audibert, Martine, Fall, Fatou, Gueye, Ibrahima, Lacombe, Karine, Seydi, Moussa, Tuaillon, Edouard, Vray, Muriel, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des sciences de la santé publique [Marseille] (ISSPAM), Aix-Marseille Sciences Economiques (AMSE), École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation [Dakar, Sénégal] (IRESSEF), ALPHABIO - Laboratoire de biologie médicale, Hôpital Européen [Fondation Ambroise Paré - Marseille], Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Université Paris Cité (UPCité)-Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), ANRS 12356 AmBASS Survey Study Group: Cyril Bérenger, Marwan Al Qays Bousmah, Sylvie Boyer, Patrizia Carrieri, Marion Coste, Maëlle de Seze, Tchadine Djaogol, Gwenaëlle Maradan, Fabienne Marcellin, Carole Treibich, Elhadji Ba, Aldiouma Diallo, Fambaye Dièye, Assane Diouf, Elhadji Bilal Faye, Assane Ndiaye, Lauren Périères, Cheikh Sokhna, Mouhamadou Baba Sow, Coumba Touré Kane, Gora Lo, Anna Julienne Selbé Ndiaye, Samba Ndiour, Philippe Halfon, Sofiane Mohamed, Nicolas Rouveau, Maria-Camila Calvo Cortès, Gabrièle Laborde-Balen, Martine Audibert, Fatou Fall, Ibrahima Gueye, Karine Lacombe, Moussa Seydi, Yusuke Shimakawa, Edouard Tuaillon, Muriel Vray, Lhuillier, Elisabeth, and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)
Subjects: Adult, Hepatitis B Surface Antigens, Adolescent, Hepatology, Vaccination, Infant, Hepatitis B, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Senegal, 3. Good health, Young Adult, 03 medical and health sciences, Cross-Sectional Studies, 0302 clinical medicine, Humans, Female, Hepatitis B Vaccines, 030211 gastroenterology & hepatology, 030212 general & internal medicine, [SHS.ECO] Humanities and Social Sciences/Economics and Finance, Child
Abstract: International audience; Senegal introduced the infant hepatitis B virus (HBV) vaccination in 2004 and recently committed to eliminating hepatitis B by 2030. Updated epidemiological data are needed to provide information on the progress being made and to develop new interventions. We estimated the prevalence of hepatitis B surface antigen (HBsAg) in children and adults living in rural Senegal and assessed hepatitis B treatment eligibility. A cross-sectional population-based serosurvey of HBsAg was conducted in 2018-2019 in a large sample (n = 3,118) of residents living in the Niakhar area (Fatick region, Senegal). Individuals positive for HBsAg subsequently underwent clinical and biological assessments. Data were weighted for age and sex and calibrated to be representative of the area's population. Among the 3,118 participants, 206 were HBsAg positive (prevalence, 6.9%; 95% confidence interval [CI], 5.6-8.1). Prevalence varied markedly according to age group in individuals aged 0-4, 5-14, 15-34, and >= 35 years as follows: 0.0% (95% CI, 0.00-0.01); 1.5% (95% CI, 0.0-2.3); 12.4% (95% CI, 9.1-15.6); and 8.8% (95% CI, 6.1-11.5), respectively. Of those subsequently assessed, 50.9% (95% CI, 41.8-60.0) had active HBV infection; 4 (2.9%; 95% CI, 0.9-9.4) were eligible for hepatitis B treatment. Conclusion: In this first population-based serosurvey targeting children and adults in rural Senegal, HBsAg prevalence was very low in the former, meeting the World Health Organization's (WHO) < 1% HBsAg 2020 target; however, it was high in young adults (15-34 years old) born before the HBV vaccine was introduced in 2004. To reach national and WHO hepatitis elimination goals, general population testing (particularly for adolescents and young adults), care, and treatment scale-up need to be implemented.
Published: 2021
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6. Prevalence and Factors Associated with Maternal Group B Streptococcus Colonization in Madagascar and Senegal

Author: Sophie Goyet, Zafitsara Zo Andrianirina, Abdoulaye Seck, Jean-Baptiste Diouf, Yu-Jin Jung, Fatoumata Diene Sarr, Perlinot Herindrainy, Elisabeth Delaroque-Astagneau, Jean-Marc Collard, Arnaud Firon, Patrick Trieu-Cuot, Bich-Tram Huynh, Raymond Bercion, Muriel Vray, Didier Guillemot, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Pharmacoépidémiologie et maladies infectieuses, Institut Pasteur [Paris], Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Institut Pasteur de Madagascar, Centre Hospitalier de Soavinandriana (CENHOSOA), Biologie des Bactéries pathogènes à Gram-positif - Biology of Gram-Positive Pathogens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur du Cambodge, Université Paris Saclay (COmUE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut National de la Santé et de la Recherche Médicale (INSERM), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), This study was supported by the Total Foundation,the African Center for Maternal and Child Health (Centre d’ExcellenceAfricainpour la Santée de la Mere et de l’Enfant),and by the Departmentof International Cooperation of the Principality of Monaco, We are grateful to all the mothers and their new-borns for their participation. We thank all physicians, laboratory staff,field interviewers, and community workers for their involvement inthis project. We thank all collaborators of the BIRDY program: Lau-rence Borand, Marguerite Diatta, Pape Samba Dieye, Joseph Faye,Beno^ıt Garin, Amy Gassama Sow (deceased), Alexandra Kerleguer,Elsa Kermorvant-Duchemin, Siyin Lach, Agathe de Lauzanne, BouyaNdao,AbibatouNdiaye,VeroniqueNgo,MichaelPadget,PatricePiola,Feno Manitra, Jacob Rakotoarimanana, Bodonirina Tanjona Raheliar-ivao, Frederique Randrianirina, Vincent Richard, Maud Seguy, BallaSy, Arnaud Tarantola, Sok Touch, Laurence Watier, and Abdou ArmyaYoussouf. We also thank Tania Crucitti for her precious advice on thecontent of the manuscript., Institut Pasteur [Paris] (IP), Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris Cité (UPCité)-Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), and HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)
Subjects: Adult, medicine.medical_specialty, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Mothers, Sociodemographic data, medicine.disease_cause, Article, Group B, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Pregnancy, Streptococcal Infections, Virology, Madagascar, Prevalence, medicine, Humans, Colonization, 030212 general & internal medicine, Pregnancy Complications, Infectious, Risk factor, reproductive and urinary physiology, Streptococcus, Obstetrics, business.industry, Infant, Newborn, Senegal, 3. Good health, Infectious Diseases, Maternal Exposure, Population Surveillance, Cohort, Obstetric history, Vaginal swabs, Female, Parasitology, Pregnant Women, business
Abstract: Maternal group B Streptococcus (GBS) colonization is a major risk factor for neonatal GBS infection. However, data on GBS are scarce in low- and middle-income countries. Using sociodemographic data and vaginal swabs collected from an international cohort of mothers and newborns, this study aimed to estimate the prevalence of GBS colonization among pregnant women in Madagascar (n = 1,603) and Senegal (n = 616). The prevalence was 5.0% (95% CI, 3.9–6.1) and 16.1% (95% CI, 13.1–19.0) in Madagascar and Senegal, respectively. No factors among sociodemographic characteristics, living conditions, and obstetric history were found to be associated independently with GBS colonization in both countries. This community-based study provides one of the first estimates of maternal GBS colonization among pregnant women from Madagascar and Senegal.
Published: 2021
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7. Changes in Intraspecific Diversity of the Arbuscular Mycorrhizal Community Involved in Plant–Plant Interactions Between Sporobolus robustus Kunth and Prosopis juliflora (Swartz) DC Along an Environmental Gradient

Author: Cheikh Ndiaye, Diégane Diouf, Fatoumata Fall, Dioumacor Fall, Estelle Tournier, Niokhor Bakhoum, Hervé Sanguin, Amadou Moustapha Bâ, Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE), Institut de Recherche pour le Développement (IRD), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université du Sine Saloum El-Hadj Ibrahima NIASS (USSEIN), and Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM)
Subjects: 0106 biological sciences, Salinity, Cebinae, Arbuscular mycorrhizal fungi, 01 natural sciences, Interactions biologiques, Soil, Prosopis, Mycorrhizae, Tolérance au sel, Colonization, Soil Microbiology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 2. Zero hunger, 0303 health sciences, Rhizosphere, Ecology, biology, Illumina sequencing, food and beverages, Vegetation, Plants, Communauté végétale, F40 - Écologie végétale, F60 - Physiologie et biochimie végétale, Relation plante sol, Soil Science, Poaceae, Intraspecific competition, 03 medical and health sciences, Glomeraceae, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arbuscular mycorrhiza [EN], Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Environmental gradient, Prosopis juliflora, 15. Life on land, biology.organism_classification, Sol salin, Plant-plant interactions, Species richness, 010606 plant biology & botany
Abstract: International audience; The intensification of biological processes coping with salt stress became a major issue to mitigate land degradation. The Sine-Saloum Delta in Senegal is characterized by salt-affected soils with vegetation dominated by salt-tolerant grass Sporobolus robustus and shrubs like Prosopis juliflora. Plant experiments in controlled conditions suggested that arbuscular mycorrhizal (AM) fungi might be the key actors of facilitation process observed between S. robustus and P. juliflora, but the AM fungal community determinants are largely unknown. The current field-based study aimed at (1) characterizing the environmental drivers (rhizosphere physico-chemical properties, plant type and season) of the AM fungal community along an environmental gradient and (2) identifying the AM fungal taxa that might explain the S. robustus-mediated benefits to P. juliflora. Glomeraceae predominated in the two plants, but a higher richness was observed for S. robustus. The pH and salinity were the main drivers of AM fungal community associated with the two plants, negatively impacting richness and diversity. However, while a negative impact was also observed on mycorrhizal colonization for S. robustus, P. juliflora showed opposite colonization patterns. Furthermore, no change was observed in terms of AM fungal community dissimilarity between the two plants along the environmental gradient as would be expected according to the stress-gradient and complementary hypotheses when a facilitation process occurs. However, changes in intraspecific diversity of shared AM fungal community between the two plants were observed, highlighting 23 AM fungal OTUs associated with both plants and the highest salinity levels. Consequently, the increase of their abundance and frequency along the environmental gradient might suggest their potential role in the facilitation process that can take place between the two plants. Their use in ecological engineering could also represent promising avenues for improving vegetation restoration in saline Senegalese's lands.
Published: 2021
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8. HIV pre-exposure prophylaxis for men who have sex with men in west Africa: a multicountry demonstration study

Author: Christian Laurent, Bintou Dembélé Keita, Issifou Yaya, Gwenvael Le Guicher, Luis Sagaon-Teyssier, Mawuényégan K Agboyibor, Alou Coulibaly, Issa Traoré, Jean-Baptiste Malan, Irith De Baetselier, August Eubanks, Lucas Riegel, Daniela Rojas Castro, Hortense Fayé-Ketté, Amadou Koné, Souba Diandé, Claver A Dagnra, Laetitia Serrano, Fodié Diallo, Ephrem Mensah, Ter Tiero E Dah, Camille Anoma, Bea Vuylsteke, Bruno Spire, Sayouba Ouedraogo, Bruno Granouillac, Martine Peeters, Clotilde Couderc, Marion Mora, Gwenaëlle Maradan, Michel Bourrelly, Mohamed Mimi, Cyril Berenger, Sylvie Boyer, Paméla Palvadeau, Thijs Reyniers, Alassane Kader Maïga, Drissa Camara, Mahamadou Diarra, Aly Ouologuem, Naboh Sangaré, Abdoul Aziz Keita, Oumar Cissé, Fodé Traoré, Bréhima Abdrahamane Ouary, Ibrahima Kanta, Rachelle Kotchi, Niamkey Thomas Aka, Kpassou Julien Lokrou, Noufo Hamed Coulibaly, Ekissi Jean Armel Koffi, Dibi Frédéric N'guessan, Stéphane-Alain Babo Yoro, Adama Cissé, Ter Tiero Elias Dah, Camille Rajaonarivelo, Fayçal Rodrique Ouedraogo, Joseph Ouedraogo, Christian Coulibaly, Mamadou Ouedraogo, Ousseni Ilboudo, Abdoulazziz Traoré, Honoré Comsiambo, Mawuényégan Kouamivi Agboyibor, Anani Attisso, Anouwarsadat Kokouba, Aléda Mawuli Badjassim, Kouakou Kokouvi Selom Agbomadji, Messan Attiogbe, Kossi Jeff Yaka, Agbégnigan Lorette Ekon, Julien Bimba, Claver Anoumou Dagnra, Kokou Dominique Tegueni, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), ARCAD Santé PLUS [Bamako, Mali], Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Espoir Vie Togo [Lomé, Togo], Association African Solidarité [Ouagadougou, Burkina Faso], Espace Confiance [Abidjan, Côte d’Ivoire], Institute of Tropical Medicine [Antwerp] (ITM), Coalition PLUS [Pantin, France], Institut Pasteur de Côte d'Ivoire, Réseau International des Instituts Pasteur (RIIP), Université des sciences, des techniques et des technologies de Bamako (USTTB), Laboratoire National de Référence de la Tuberculose [Ouagadougou, Burkina Faso] (LNRT), Laboratoire National de Référence de la tuberculose [Lomé, Togo] (LNRT/CHU Lomé), CohMSM-PrEP Study Group: Christian Laurent, Issifou Yaya, Sayouba Ouedraogo, Bruno Granouillac, Gwenvael Le Guicher, Laetitia Serrano, Martine Peeters, Clotilde Couderc, Bruno Spire, Luis Sagaon-Teyssier, Marion Mora, Gwenaëlle Maradan, Michel Bourrelly, Mohamed Mimi, Cyril Berenger, Sylvie Boyer, Daniela Rojas Castro, Lucas Riegel, Paméla Palvadeau, Bea Vuylsteke, Irith De Baetselier, Thijs Reyniers, Bintou Dembélé Keita, Fodié Diallo, Alou Coulibaly, Alassane Kader Maïga, Drissa Camara, Mahamadou Diarra, Aly Ouologuem, Naboh Sangaré, Abdoul Aziz Keita, Oumar Cissé, Fodé Traoré, Bréhima Abdrahamane Ouary, Ibrahima Kanta, Camille Anoma, Jean-Baptiste Malan, Rachelle Kotchi, Niamkey Thomas Aka, Kpassou Julien Lokrou, Noufo Hamed Coulibaly, Ekissi Jean Armel Koffi, Dibi Frédéric N'guessan, Stéphane-Alain Babo Yoro, Adama Cissé, Ter Tiero Elias Dah, Issa Traoré, Camille Rajaonarivelo, Fayçal Rodrique Ouedraogo, Joseph Ouedraogo, Christian Coulibaly, Mamadou Ouedraogo, Ousseni Ilboudo, Abdoulazziz Traoré, Honoré Comsiambo, Ephrem Mensah, Mawuényégan Kouamivi Agboyibor, Anani Attisso, Anouwarsadat Kokouba, Aléda Mawuli Badjassim, Kouakou Kokouvi Selom Agbomadji, Messan Attiogbe, Kossi Jeff Yaka, Agbégnigan Lorette Ekon, Julien Bimba, Claver Anoumou Dagnra, Kokou Dominique Tegueni, Malbec, Odile, Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), and Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI)
Subjects: Adult, Male, 0301 basic medicine, Anti-HIV Agents, Epidemiology, Sexual Behavior, [SDV]Life Sciences [q-bio], Immunology, HIV Infections, Pilot Projects, Emtricitabine, Men who have sex with men, West africa, Young Adult, 03 medical and health sciences, Pre-exposure prophylaxis, 0302 clinical medicine, Virology, parasitic diseases, Humans, Medicine, Prospective Studies, 030212 general & internal medicine, Dosing, Homosexuality, Male, Tenofovir, Prospective cohort study, business.industry, 1. No poverty, 030112 virology, 3. Good health, [SDV] Life Sciences [q-bio], Africa, Western, Regimen, Infectious Diseases, Cohort, Pre-Exposure Prophylaxis, business, Demography, medicine.drug
Abstract: International audience; Background HIV pre-exposure prophylaxis (PrEP) data in men who have sex with men (MSM) in west Africa are essential to guide its large-scale implementation. We assessed the uptake of event-driven and daily PrEP, HIV incidence, and changes over time in sexual behaviours and prevalence of bacterial sexually transmitted infections (STIs) in MSM in Burkina Faso, Côte d'Ivoire, Mali, and Togo. Methods We did a prospective cohort study from Nov 20, 2017, to April 14, 2020, in four community-based clinics in Abidjan (Côte d'Ivoire), Bamako (Mali), Lomé (Togo), and Ouagadougou (Burkina Faso). Participants were MSM aged 18 years or older at substantial risk of HIV infection. Participants could choose between event-driven (2+1+1 dosing) and daily oral PrEP (tenofovir disoproxil fumarate 300 mg plus emtricitabine 200 mg), switch regimen, and discontinue or restart PrEP. We compared HIV incidence in this study with that of the same cohort before the availability of PrEP (CohMSM). Statistical analysis included the Kaplan-Meier method and mixed-effects regression models. This study is registered with ClinicalTrials.gov, NCT03459157. Findings We followed up 598 participants for a total of 743•6 person-years. At enrolment, 445 (74%) of 598 participants chose event-driven PrEP and 153 (26%) of 598 chose daily PrEP. 60 (13%) of 445 and 65 (42%) of 153 partici pants switched PrEP regimen at least once (p
Published: 2021
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9. Gut microbiota changes after metabolic surgery in adult diabetic patients with mild obesity: a randomised controlled trial

Author: Isaac Barroso, Isabel M. Miranda, Davide Carvalho, Paula Freitas, Maria Manuel Silva, Paul Picq, Eva Lau, Adelino Barbosa, Flora Correia, Joël Doré, Edi Prifti, Karine Clément, Cidália Pina Vaz, Eugeni Belda, Manuel Ferreira-Magalhães, Universidade do Porto = University of Porto, Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Instituto de Investigação e Inovação em Saúde (I3S), Nutrition et obésités: approches systémiques (UMR-S 1269) (Nutriomics), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), MetaGenoPolis (MGP (US 1367)), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord]), Faculdade de Ciências da Nutrição e Alimentação, Faculdade de Medicina, Universidade do Porto, Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Nutrition et obésités: approches systémiques (nutriomics) (UMR-S 1269 INSERM - Sorbonne Université), and Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU)
Subjects: 0301 basic medicine, medicine.medical_specialty, Weight loss, RC620-627, Roux-en-Y gastric bypass, [SDV]Life Sciences [q-bio], Endocrinology, Diabetes and Metabolism, Gut flora, Gastroenterology, law.invention, 03 medical and health sciences, 0302 clinical medicine, Insulin resistance, Diabetes mellitus, Randomized controlled trial, law, Internal medicine, Internal Medicine, Medicine, Microbiome, Nutritional diseases. Deficiency diseases, 2. Zero hunger, biology, business.industry, Research, Health sciences, Medical and Health sciences, Ciências médicas e da saúde, nutritional and metabolic diseases, medicine.disease, biology.organism_classification, Obesity, 3. Good health, Clinical trial, 030104 developmental biology, 030220 oncology & carcinogenesis, Medical and Health sciences, Ciências da Saúde, Ciências médicas e da saúde, medicine.symptom, business
Abstract: Background Roux-en-Y gastric bypass (RYGB) surgery is one of the most efficient procedures for the treatment of obesity, also improving metabolic and inflammatory status, in patients with mild obesity. The underlying mechanisms have not been fully understood, but gut microbiota is hypothesized to play a key role. Our aim was to evaluate the association between gut microbiota changes and anthropometric, metabolic and inflammatory profiles after metabolic surgery compared with medical therapy, in type 2 diabetic (T2DM) adults with mild obesity (BMI 30–35 kg/m2). Methods DM2 was an open-label, randomised controlled clinical trial (RCT: ISRCTN53984585) with 2 arms: (i) surgical, and (ii) medical. The main outcome was gut microbiota changes after: metabolic surgery (Roux-en-Y gastric bypass—RYGB) versus standard medical therapy. Secondary outcomes included anthropometric, metabolic and inflammatory profiles. Clinical visits, blood workup, and stool samples were collected at baseline and months (M)1, 3, 6, 12. Gut microbiota was profiled using 16S rRNA targeted sequencing. Results Twenty patients were included: 10 in surgical and 10 in medical arm. Anthropometric and metabolic comparative analysis favoured RYGB over medical arm. At M12, the percentage of weight loss was 25.5 vs. 4.9% (p p p = 0.004, [R2 = 0.17]) during the follow-up period after RYGB. There was a strong association between improvement of anthropometric/metabolic/inflammatory biomarkers and increase in microbial richness and Proteobacterial lineages. Conclusions This was the first RCT studying composite clinical, analytic, and microbiome changes in T2DM patients with class 1 obesity after RYGB versus standard medical therapy. The remarkable phenotypic improvement after surgery occurred concomitantly with changes in the gut microbiome, but at a lower level. Trial registration: ISRCTN53984585
Published: 2021
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10. Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo

Author: Francois Edidi-Atani, Moussa Moïse Diagne, Meris Matondo-Kuamfumu, Junior Bulabula, Kristian G. Andersen, Bibiche Nsunda, Eric Delaporte, Bailey White, Amadou A. Sall, Trevor Bedford, Matthias Pauthner, Martine Peeters, Nella Bisento, Jean Jacques Muyembe Tamfum, Marceline Akonga, James Hadfield, Daniel Mukadi, Michael R. Wiley, Gustavo Palacios, Fabrice Mambu-Mbika, Amuri Aziza, Nicholas Di Paola, Steve Ahuka-Mundeke, Eddy Kinganda-Lusamaki, Catherine Pratt, Ousmane Faye, Martin Faye, Allison Black, Placide Mbala-Kingebeni, University of Kinshasa (UNIKIN), Institut National de Recherche Biomédicale [Kinshasa] (INRB), University of Washington [Seattle], Fred Hutchinson Cancer Research Center [Seattle] (FHCRC), University of Nebraska Medical Center, University of Nebraska System, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), The Scripps Research Institute [La Jolla, San Diego], Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), and Retiveau, Nolwenn
Subjects: 0301 basic medicine, MESH: Sequence Analysis, DNA, medicine.medical_specialty, Genomic data, MESH: Reinfection, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Genome, Viral, Disease, medicine.disease_cause, Genome, Article, General Biochemistry, Genetics and Molecular Biology, Disease Outbreaks, 03 medical and health sciences, MESH: Spatio-Temporal Analysis, Spatio-Temporal Analysis, 0302 clinical medicine, Recurrence, Environmental health, MESH: Congo, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, medicine, MESH: Ebola Vaccines, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Disease Outbreaks, MESH: Ebolavirus, Ebola Vaccines, MESH: Phylogeny, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Phylogeny, Ebola virus, Transmission (medicine), MESH: Genomics, Genomic sequencing, Public health, Outbreak, Genomics, Sequence Analysis, DNA, General Medicine, Hemorrhagic Fever, Ebola, Ebolavirus, MESH: Recurrence, 030104 developmental biology, Geography, Congo, Reinfection, 030220 oncology & carcinogenesis, MESH: Hemorrhagic Fever, Ebola, MESH: Genome, Viral
Abstract: On 1 August 2018, the Democratic Republic of the Congo (DRC) declared its tenth Ebola virus disease (EVD) outbreak. To aid the epidemiologic response, the Institut National de Recherche Biomedicale (INRB) implemented an end-to-end genomic surveillance system, including sequencing, bioinformatic analysis and dissemination of genomic epidemiologic results to frontline public health workers. We report 744 new genomes sampled between 27 July 2018 and 27 April 2020 generated by this surveillance effort. Together with previously available sequence data (n = 48 genomes), these data represent almost 24% of all laboratory-confirmed Ebola virus (EBOV) infections in DRC in the period analyzed. We inferred spatiotemporal transmission dynamics from the genomic data as new sequences were generated, and disseminated the results to support epidemiologic response efforts. Here we provide an overview of how this genomic surveillance system functioned, present a full phylodynamic analysis of 792 Ebola genomes from the Nord Kivu outbreak and discuss how the genomic surveillance data informed response efforts and public health decision making. Phylogeographic analysis of 792 Ebola virus genomes from the 2018 oubreak in the Democratic Republic of the Congo integrated into an end-to-end surveillance program demonstrates the feasibility of using genomic sequencing data to inform the public health epidemic response in near-real time.
Published: 2021
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11. The Impact of Renewing Long-Lasting Insecticide-Treated Nets in the Event of Malaria Resurgence: Lessons from 10 Years of Net Use in Dielmo, Senegal

Author: Souleymane Doucoure, Nafissatou Diagne, Amélé N. Wotodjo, Cheikh Sokhna, Philippe Parola, Jean Gaudart, Fatoumata Diene Sarr, Maladies infectieuses persistantes et émergentes en Afrique de l’Ouest [Dakar, Sénégal] (Equipe 3 - VITROME), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Unité d'Epidémiologie des Maladies Infectieuses, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Malaria Research and Training Center [Bamako, Mali], Université de Bamako, Malaria Research and Training Center-Ogobara K. Doumbo [Bamako, Mali] (MRTC-OKD), Université des sciences, des techniques et des technologies de Bamako (USTTB), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biostatistique et technologies de l'information et de la communication (BioSTIC) - [Hôpital de la Timone - APHM] (BiosTIC ), Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Dupuis, Christine, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)
Subjects: Adult, Male, Long lasting, Mosquito Control, Adolescent, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Rate ratio, Disease Outbreaks, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Virology, parasitic diseases, medicine, Humans, 030212 general & internal medicine, Insecticide-Treated Bednets, Child, Insecticide treated nets, 2. Zero hunger, 1. No poverty, Infant, Articles, Middle Aged, medicine.disease, Senegal, Malaria, 3. Good health, Universal coverage, [SDV] Life Sciences [q-bio], Infectious Diseases, Geography, Child, Preschool, Female, Parasitology, Demography
Abstract: International audience; The occurrence of malaria resurgences could threaten progress toward elimination of the disease. This study investigated the impact of repeated renewal of long-lasting insecticide-treated net (LLIN) universal coverage on malaria resurgence over a period of 10 years of net implementation in Dielmo (Senegal). A longitudinal study was carried out in Dielmo between August 2007 and July 2018. In July 2008, LLINs were offered to all villagers through universal campaign distribution which was renewed in July 2011, August 2014, and May 2016. Malaria cases were treated with artemisinin-based combination therapy. Two resurgences of malaria occurred during the 10 years in which LLINs have been in use. Since the third renewal of the nets, malaria decreased significantly compared with the first year the nets were implemented (adjusted incidence rate ratio) (95% CI) = 0.35 (0.15-0.85), during the ninth year after net implementation). During the tenth year of net implementation, no cases of malaria were observed among the study population. The use of nets increased significantly after the third time the nets were renewed when compared with the year after the first and the second times the nets were renewed (P < 0.001). The third renewal of nets, which took place after 2 years instead of 3 years together with a higher use of LLINs especially among the young, probably prevented the occurrence of a third malaria upsurge in this village.
Published: 2021
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12. Renal impairment assessment on adults living nearby a landfill: Early kidney dysfunction biomarkers linked to the environmental exposure to heavy metals

Author: Fabrice Cazier, Fatoumata Bah, Saâd Bouhsina, Guillaume Garçon, Anthony Verdin, Mathilde Cabral, Aminata Toure, Mamadou Fall, Dorothée Dewaele, Adama Faye, Dominique Courcot, CHU Lille, Institut Pasteur de Lille, Université de Lille, Unité de Chimie Environnementale et Interactions sur le Vivant [UCEIV], IMPact de l'Environnement Chimique sur la Santé humaine (IMPECS) - ULR 4483, Université du Littoral Côte d'Opale [ULCO], Université Cheikh Anta Diop [Dakar, Sénégal] [UCAD], Impact de l'environnement chimique sur la santé humaine - ULR 4483 [IMPECS], Centre commun de mesures [CCM-ULCO], Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d'Opale (ULCO), Impact de l'environnement chimique sur la santé humaine - ULR 4483 (IMPECS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), and Centre commun de mesures (CCM-ULCO)
Subjects: medicine.medical_specialty, [SDV]Life Sciences [q-bio], Health, Toxicology and Mutagenesis, Urinary system, Population, 010501 environmental sciences, Lipocalin, Toxicology, 01 natural sciences, Nephrotoxicity, 03 medical and health sciences, 0302 clinical medicine, RA1190-1270, Internal medicine, medicine, Biomarkers, Cadmium, Landfill, Lead, education, ComputingMethodologies_COMPUTERGRAPHICS, 0105 earth and related environmental sciences, Kidney, education.field_of_study, Beta-2 microglobulin, business.industry, Regular Article, Environmental exposure, Retinol binding protein, medicine.anatomical_structure, Endocrinology, Toxicology. Poisons, business, 030217 neurology & neurosurgery
Abstract: Graphical abstract, Highlights • Health risk of the neighboring population of the Mbeubeuss landfill (Senegal). • Assessment of the impact of Cd/Pb exposure through dysfunction renal biomarkers. • Specific increases of a set of early dysfunction renal biomarkers in exposed subjects. • Glomerular and tubular dysfunction in exposed subjects., The aim of this study was to assess the integrity and kidney overall functional capacity of subjects exposed to landfill emissions. Urine and blood levels of Pb and Cd, and several of the newly biomarkers of nephrotoxicity (Kim Injury Molecule 1 (KIM-1), alpha-1 Microglobulin (α1 M), beta-2 Microglobulin (β2 M), Cystatin-C (Cyst C), Clusterin, alpha-glutathione S-transferase (GSTα), pi-glutathione S-transferase (GSTπ), Tissue Inhibitor of Metalloproteinase-1 (TIMP1), Calbindin, Neutrophil Gelatinase-Associated Lipocalin (NGAL), Osteopontin (OPN), (Retinol Binding Protein(RBP), Liver-type Fatty Acid-Binding Protein (FABP-1), Trefoil Factor 3 (TFF3), Collagen VI) were measured in order to assess glomerular and tubule damage in adults living near a landfill. Our results indicate glomerular dysfunction in exposed subjects, and supported evidence of necrosis of proximal and distal tubule epithelial cells as specific biomarkers began to appear in the urine. Positive correlation by Pearson test were obtained between : blood Pb and B-OPN, B-Cyst C, Calbindin, U-KIM-1, TIMP1, U-OPN, and U-Clusterin; and also, between urinary Cd and TIMP1, B-Clusterin, U-OPN, FABP-1, Albumin, and U-Clusterin. The relation between biomarkers of Cd/Pb exposure and early effect biomarkers in this study clearly predicts the future risk of severe kidney injury in subjects living close to the landfill.
Published: 2021
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13. Cost-Utility Analysis of a Dolutegravir-Based Versus Low-Dose Efavirenz-Based Regimen for the Initial Treatment of HIV-Infected Patients in Cameroon (NAMSAL ANRS 12313 Trial)

Author: Marie Libérée Nishimwe, Marie Varloteaux, Charles Kouanfack, Eric Delaporte, Alice Montoyo, Sylvie Boyer, Martial Lantche Wandji, Pierrette Omgba Bassega, Mireille Mpoudi-Etame, Gwenaëlle Maradan, Marwân-al-Qays Bousmah, Tamara Tovar-Sanchez, Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Agence Nationale de Recherches sur le Sida et les Hépatites Virales (ANRS), Hôpital Central de Yaoundé [Yaoundé], Hôpital Militaire de Yaoundé, Partenaires INRAE, Hôpital de la Cité Verte [Yaoundé], Université de Dshang, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), and Herrada, Anthony
Subjects: Adult, Cyclopropanes, medicine.medical_specialty, Pediatrics, Efavirenz, Pyridones, Cost-Benefit Analysis, HIV Infections, JEL: I - Health, Education, and Welfare/I.I1 - Health/I.I1.I19 - Other, Piperazines, Health administration, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Oxazines, Humans, Medicine, Original Research Article, Cameroon, 030212 general & internal medicine, [SHS.ECO] Humanities and Social Sciences/Economics and Finance, Pharmacology, Cost–utility analysis, Health economics, business.industry, 030503 health policy & services, Health Policy, Public health, Public Health, Environmental and Occupational Health, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Benzoxazines, 3. Good health, Regimen, chemistry, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Alkynes, Dolutegravir, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Anxiety, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, medicine.symptom, 0305 other medical science, business, Heterocyclic Compounds, 3-Ring
Abstract: Objectives Evidence comparing the economic and patient values of the World Health Organization’s preferred (dolutegravir 50 mg [DTG]-based) and alternative (low-dose [400 mg] efavirenz [EFV400]-based) first-line antiretroviral regimens is limited. We compared patient-reported outcomes (PROs), costs, and the cost-utility of DTG- versus EFV400-based regimens in treatment-naive HIV-1 adults in the randomised NAMSAL ANRS 12313 trial in Yaoundé, Cameroon. Methods We used clinical data, PROs, and health resource use data collected in the trial’s first 96 weeks (2016–2019). Quality-adjusted life-years (QALYs) were computed using utility scores obtained from the 12-item Short Form (SF-12) generic health scale. Other PROs included perceived symptoms, depression, anxiety, and stress. In the 96-week base-case analysis, we estimated the unadjusted and multivariate-adjusted (1) mean costs (in US$, 2016 values) and QALYs/patient, (2) incremental costs and QALYs/patient, and (3) net health benefit (NHB). Outcomes were extrapolated over 5 and 10 years. Uncertainty was assessed using the cost-effectiveness acceptability curve and scenario and cost-effective price threshold analyses. Results In the base-case analysis, the NHB (95% confidence interval) for the DTG-based regimen relative to the EFV400-based regimen was 0.056 (− 0.037 to 0.153), corresponding to an 88% probability of DTG being cost-effective. A 10% decrease in this regimen’s price (from $5.2 to $4.7/month) would increase its cost-effectiveness probability to 95%. When extrapolating outcomes over 5 and 10 years, the DTG-based regimen had a 100% probability of being cost-effective for a large range of cost-effectiveness thresholds. Conclusions At 2020 antiretroviral drug prices, a DTG-based first-line regimen should be preferred over an EFV400-based regimen in sub-Saharan Africa. Trial Registration ClinicalTrials.gov Identifier: NCT02777229. Supplementary Information The online version contains supplementary material available at 10.1007/s40273-020-00987-3.
Published: 2020
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14. Type 1 Diabetes in People Hospitalized for COVID-19: New Insights From the CORONADO Study

Author: Sandrine Lablanche, Florence Galtier, Pierre Leroy, Vincent Dubée, Dominique Bonnefont-Rousselot, Patrick Saulnier, Matthieu Wargny, Manuel Etienne, Patrice Darmon, Anne-Laure Borel, Jean-Louis LAPLANCHE, Olivier Lesieur, Bertrand Cariou, Malak Taher, Lydia GUITTET, Vincent Minville, BRUNO MOURVILLIER, Jean-Pierre QUENOT, Bernard Bonnotte, Lucien Marchand, Team2 Carmen, Veronique Kerlan, Pascal Reynier, Nadia Sabbah, Matthieu PICHELIN, Jean-Charles Aurégan, Guillaume Martin-Blondel, Olivier Bourron, Blandine Rammaert, Pierre-Edouard Fournier, Coralie Amadou, Giulia Chinetti, Jean-Christophe Lagier, Didier Raoult, Centre hospitalier universitaire de Nantes (CHU Nantes), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Hôpital de la Conception [CHU - APHM] (LA CONCEPTION), Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Hospitalier Sud Francilien, Unité de recherche de l'institut du thorax (ITX-lab), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Service d'endocrinologie, diabétologie et nutrition [CHU Bichat], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Cité (UPCité), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hôpital Lariboisière-Fernand-Widal [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Pathogénèse et contrôle des infections chroniques (PCCI), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Diabétologie [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université de Paris (UP), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), CH Evry-Corbeil, unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université de Paris (UP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Service de diabétologie [CHU Pitié-Salpétrière], Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Paris (UP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Gestionnaire, Hal Sorbonne Université
Subjects: Male, Pediatrics, medicine.medical_specialty, [SDV]Life Sciences [q-bio], Endocrinology, Diabetes and Metabolism, Pneumonia, Viral, Population, 030209 endocrinology & metabolism, law.invention, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, law, Diabetes mellitus, Internal Medicine, medicine, Clinical endpoint, Humans, 030212 general & internal medicine, education, Pandemics, Case report form, ComputingMilieux_MISCELLANEOUS, Aged, Aged, 80 and over, Glycated Hemoglobin, Advanced and Specialized Nursing, Inpatients, Type 1 diabetes, education.field_of_study, business.industry, e-Letters: Observations, COVID-19, Middle Aged, Prognosis, medicine.disease, Respiration, Artificial, Intensive care unit, 3. Good health, [SDV] Life Sciences [q-bio], Diabetes Mellitus, Type 2, Hypertension, Etiology, Female, Observational study, Coronavirus Infections, business
Abstract: Since the start of the coronavirus disease 2019 (COVID-19) pandemic, patients with diabetes were rapidly recognized as a high-risk population for severe disease. Indeed, a high prevalence of diabetes among patients with COVID-19 who required hospitalization has been consistently reported, reaching 33.8% in 5,700 people hospitalized for COVID-19 in the New York City area (1). In addition, diabetes was associated with more than a doubled risk of intensive care unit (ICU) admission and more than a tripled risk of death (2). However, precise data regarding the type of diabetes are scarce. We report here the clinical characteristics and early prognosis of patients with type 1 diabetes (T1D) hospitalized for COVID-19 in the nationwide multicenter observational CORONADO (Coronavirus SARS-CoV-2 and Diabetes Outcomes) study (3). The aim of the CORONADO study was to describe the phenotypic characteristics and prognosis of patients with diabetes admitted with COVID-19 between 10 March and 10 April 2020 in 68 French hospitals. The protocol (ClinicalTrials.gov reg. no. NCT04324736) obtained all regulatory approvals as recently described (3). Inclusion criteria were 1 ) hospitalization for biologically and/or clinically/radiologically attested COVID-19 and 2 ) personal history of diabetes or newly diagnosed diabetes on admission. The composite primary end point combined tracheal intubation for mechanical ventilation and/or death on day 7 (D7). Secondary outcomes included death, tracheal intubation, and discharge on D7. Classification of diabetes was recorded in the electronic case report form as noted in the medical file by the physician in charge of the patient. In the present subanalysis, patients in whom diabetes was diagnosed on admission were excluded since the etiological diagnosis had not been formally established. All cases noted as T1D were carefully reviewed by local investigators and the steering committee …
Published: 2020
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15. Rare and unique adaptations to cancer in domesticated species: An untapped resource?

Author: Dorothée Missé, Georgina Bramwell, Aaron G. Schultz, Margaux Bieuville, Beata Ujvari, Nolwenn M. Dheilly, Jérôme Abadie, Péter Biró, Sophie Labrut, Tracey Russell, Flora Gouzerh, Justine Boutry, François Renaud, Orsolya Vincze, Rodrigo Hamede, Guillaume Le Loc'h, Mathieu Giraudeau, Benjamin Roche, Frédéric Thomas, Christa Beckmann, Centre de Recherches Ecologiques et Evolutives sur le Cancer (CREEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 [Cameroun]-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord]), Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), School of Marine and Atmospheric Sciences [Stony Brook] (SoMAS), Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Deakin University, Burwood, Australia, Deakin University [Burwood], Western Sydney University, University of Tasmania [Hobart, Australia] (UTAS), Animaux modèles pour la recherche en oncologie comparée (AMaROC), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hungarian Department of Biology and Ecology [Cluj‑Napoca, Romania], Babes-Bolyai University [Cluj-Napoca] (UBB), MTA Centre for Ecological Research [Tihany], Hungarian Academy of Sciences (MTA), Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU), The University of Sydney, This work was supported by an ARC Linkage (LP170101105), Deakin SEBE_RGS_2019, an ANR TRANSCAN (ANR-18-CE35-0009) and a CNRS 'International Associated Laboratory Grant.' Support was also provided by the Rotary Club Les Sables d’Olonne to FT. OV is supported by the Romanian Ministry of Research and Innovation (PN-III-P4-ID-PCE-2016-0404), by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences and by the New National Excellence Program of the Ministry of Innovation and Technology (ÚNKP-19-4-DE-538)., ANR-18-CE35-0009,TRANSCAN,ECOLOGIE ET EVOLUTION DES CANCERS TRANSMISSIBLES(2018), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord])
Subjects: 0106 biological sciences, 0301 basic medicine, evolutionary mismatch, Resource (biology), [SDV]Life Sciences [q-bio], domestication syndrome, lcsh:Evolution, selection, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, domestication, evolutionary, evolution, Genetics, Inbreeding depression, medicine, lcsh:QH359-425, cancer, Domestication, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), High rate, Cancer, Mismatch theory, medicine.disease, 030104 developmental biology, Evolutionary biology, General Agricultural and Biological Sciences, mismatch
Abstract: International audience; Strong and ongoing artificial selection in domestic animals has resulted in amazing phenotypic responses that benefit humans, but often at a cost to an animal's health, and problems related to inbreeding depression, including a higher incidence of cancer. Despite high rates of cancer in domesticated species, little attention has been devoted to exploring the hypothesis that persistent artificial selection may also favour the evolution of compensatory anticancer defences. Indeed, there is evidence for effective anti‐cancer defences found in several domesticated species associated with different cancer types. We also suggest that artificial selection can favour the “domestication” of inherited oncogenic mutations in rare instances, retaining those associated to late and/or less aggressive cancers, and that by studying these seemingly rare anticancer adaptations, novel cancer treatments may be found.
Published: 2020
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16. The interface between ecology, evolution, and cancer: More than ever a relevant research direction for both oncologists and ecologists

Author: Frédéric Thomas, Beata Ujvari, Mathieu Giraudeau, Benjamin Roche, Rodrigo Hamede, Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU), Universidad Nacional Autónoma de México (UNAM), University of Tasmania [Hobart, Australia] (UTAS), Deakin University [Burwood], Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord]), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), and ANR-18-CE35-0009,TRANSCAN,ECOLOGIE ET EVOLUTION DES CANCERS TRANSMISSIBLES(2018)
Subjects: 0106 biological sciences, conservation biology, Interface (Java), Ecology (disciplines), [SDV]Life Sciences [q-bio], lcsh:Evolution, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genetics, medicine, lcsh:QH359-425, cancer, evolutionary theory, Ecology, Evolution, Behavior and Systematics, Evolutionary theory, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Cognitive science, 0303 health sciences, Evolutionary medicine, Cancer, medicine.disease, evolutionary medicine, oncology, Conservation biology, General Agricultural and Biological Sciences
Abstract: International audience
Published: 2020
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17. Nevirapine Use Is Associated with Higher Bone Mineral Density in HIV-1 Positive Subjects on Long-Term Antiretroviral Therapy

Author: Couffignal, Camille, Kolta, Sami, Flamant, Martin, Cazanave, Charles, Haymann, Jean-Philippe, Mentre, France, Duval, Xavier, Leport, Catherine, Raffi, Francois, Chêne, G., Salamon, R., Moatti, J., Pierret, J., Spire, B., Brun-Vézinet, F., Fleury, H., Masquelier, B., Peytavin, G., Garraffo, R., Costagliola, D., Dellamonica, P., Katlama, C., Meyer, L., Salmon, D., Cuzin, L., Dupon, M., Le Moing, V., Marchou, B., May, T., Morlat, P., Rabaud, C., Waldner-Combernoux, A., Hardel, L., Reboud, P., Couffin-Cadiergues, S., Marchand, L., Assuied, A., Carrieri, P., Habak, S., Couturier, F., Jadand, C., Perrier, A., Préau, M., Protopopescu, C., Schmit, J.L., Chennebault, J.M., Faller, J.P., Magy-Bertrand, N., Chirouze, C., Humbert, P., Neau, D., Granier, P., Ansart, S., Verdon, R., Merrien, D., Chevojon, P., Sobel, A., Levy, Y., Piroth, L., Perronne, C., Froguel, E., Ceccaldi, J., Chidiac, C., Grégoire, V., Reynes, J., Fuzibet, J., Arsac, P., Bouvet, E., Bricaire, F., Monsonego, J., Girard, P.M., Guillevin, L., Herson, S., Molina, J.M., Pialoux, G., Sain, O., Sellier, P., Roblot, F., Bani-Sadr, F., Michelet, C., Lucht, F., Debord, C., Martin, T., de Jaureguiberry, J.P., Bernard, L., Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Physiologie [Bichat-Claude Bernard], Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Service des Maladies Infectieuses et Tropicales A [Bordeaux], CHU Bordeaux [Bordeaux]-Groupe hospitalier Pellegrin, Remodelage et Reparation du Tissu Renal, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), CIC Hôpital Bichat, AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-UFR de Médecine, Modèles et méthodes de l'évaluation thérapeutique des maladies chroniques (U738 / UMR_S738), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre hospitalier universitaire de Nantes (CHU Nantes), Epidémiologie, santé publique et développement, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Santé Publique, Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Microbiologie Fondamentale et Pathogénicité (MFP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Pharmacie de l'Hôpital Bichat, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Service des maladies infectieuses, Centre Hospitalier Universitaire de Nice (CHU Nice)-University Hospital, CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Bordeaux [Bordeaux], Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Bell Labs (BELL), Lucent Technologies, Service des Maladies Infectieuses et Tropicales [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), CHU Amiens-Picardie, Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), service de maladies infectieuses CHU J Minjoz Besancon, Service de virologie et d'immunologie biologique, Hôpital de la Cavale Blanche - CHRU Brest (CHU - BREST ), Unité de Maladies Infectieuses et Tropicales [CHU Caen], Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Tumorothèque de Caen Basse-Normandie (TCBN), Département d'infectiologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Service des Maladies Infectieuses et Tropicales [CHU Raymond Poincaré], Hôpital Raymond Poincaré [AP-HP], Centre Hospitalier Libourne, Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Department of Radiation Oncology, Université Catholique de Louvain = Catholic University of Louvain (UCL), GERES - Groupe d'Étude sur le Risque d'Exposition des Soignants aux agents infectieux - Research Group for the Prevention of Occupational Infections in Healthcare Workers [Paris, France], Service de médecine interne et centre de référence des maladies rares [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Pharmacologie des anti-infectieux (PHAR), Université de Poitiers-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Reims (CHU Reims), University Hospital and University Jean Monnet, Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Institut National de la Santé et de la Recherche Médicale (INSERM)-UFR de Médecine-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7), Microbiologie cellulaire et moléculaire et pathogénicité (MCMP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service des maladies infectieuses et tropicales [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Groupe d'Étude sur le Risque d'Exposition des Soignants aux agents infectieux (GERES), Cholley, Pascal, and Service de Maladies Infectieuses et Tropicales [CHU Pitié-Salpêtrière]
Subjects: Adult, Male, medicine.medical_specialty, Time Factors, Nevirapine, nevirapine, Immunology, Cumulative Exposure, HIV Infections, 03 medical and health sciences, Absorptiometry, Photon, 0302 clinical medicine, Bone Density, Virology, Internal medicine, medicine, Humans, Prospective Studies, 030212 general & internal medicine, 030304 developmental biology, Bone mineral, 0303 health sciences, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, business.industry, Incidence (epidemiology), HIV, virus diseases, Odds ratio, Middle Aged, medicine.disease, Confidence interval, 3. Good health, Cross-Sectional Studies, Infectious Diseases, Cohort, HIV-1, Coinfection, Reverse Transcriptase Inhibitors, Female, bone mineral density, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Follow-Up Studies, medicine.drug
Abstract: International audience; We assessed bone mineral density (BMD) in a cohort of human immunodeficiency virus (HIV)-positive patients after a median of 11 years of combination antiretroviral therapy (cART) and evaluated the respective role of HIV infection and antiretroviral drugs (ARVs). A cross-sectional study of 162 participants (131 male) from the ANRS-C08 cohort was performed with bone dual-energy X-ray absorptiometry (DXA) scans and renal assessment. The window of exposure to ARVs was defined as an exposure of more than six cumulative months during the last 3 years before the DXA evaluation to account for a cumulative exposure that could affect bone remodeling. The association with low BMD (Z-score < -2) was assessed by a multiple logistic regression model. The study population was 50 years (median), hepatitis C virus (HCV) (18%), and hepatitis B virus (HBV) (8%) coinfection with HIV-RNA
Published: 2020
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18. Negotiating Intersecting Precarities: COVID-19, Pandemic Preparedness and Response in Africa

Author: Hayley MacGregor, Melissa Leach, Grace Akello, Lawrence Sao Babawo, Moses Baluku, Alice Desclaux, Catherine Grant, Foday Kamara, Fred Martineau, Esther Yei Mokuwa, Melissa Parker, Paul Richards, Kelley Sams, Khoudia Sow, Annie Wilkinson, University of Sussex, Gulu University, Partenaires INRAE, Njala University, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), London School of Hygiene and Tropical Medicine (LSHTM), University of Florida [Gainesville] (UF), Laboratoire Population-Environnement-Développement (LPED), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut de Recherche pour le Développement (IRD), Centre Norbert Elias (CNELIAS), École des hautes études en sciences sociales (EHESS)-Avignon Université (AU)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre Régional de recherche et de Formation à la prise en charge Clinique de Fann (CRCF), CHNU Fann, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), École des hautes études en sciences sociales (EHESS)-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), and Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)
Subjects: 060101 anthropology, Health (social science), response, Preparedness, Negotiating, SARS-CoV-2, Anthropology, Medical, COVID-19, 06 humanities and the arts, [SHS.ANTHRO-SE]Humanities and Social Sciences/Social Anthropology and ethnology, epidemic, precarity, 03 medical and health sciences, 0302 clinical medicine, Anthropology, Africa, Humans, 0601 history and archaeology, 030212 general & internal medicine, Pandemics, Research Articles, Research Article
Abstract: International audience; This article shares findings on COVID-19 in Africa across 2020 to examine concepts and practices of epidemic preparedness and response. Amidst uncertainties about the trajectory of COVID-19, the stages of emergency response emerge in practice as interconnected. We illustrate how complex dynamics manifest as diverse actors interpret and modify approaches according to contexts and experiences. We suggest that the concept of "intersecting precarities" best captures the temporalities at stake; that these precarities include the effects of epidemic control measures; and that people do not just accept but actively negotiate these intersections as they seek to sustain their lives and livelihoods.
Published: 2022
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19. Fine-scale Spatiotemporal Mapping of Asymptomatic and Clinical Plasmodium falciparum Infections: Epidemiological Evidence for Targeted Malaria Elimination Interventions

Author: Nafissatou Diagne, Adja Fatou Mbodj, Laty G. Thiam, Cheikh Talla, Mirco Sandfort, Ivo Mueller, Aissatou Toure-Balde, Inès Vigan-Womas, Cheikh Sokhna, Joseph Faye, Abdoulaye Badiane, Rokhaya Sane, Michael T. White, Babacar Diouf, Thiam A, Makhtar Niang, Fatoumata Diene Sarr, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Malaria : parasites et hôtes - Malaria : parasites and hosts, Institut Pasteur [Paris], Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Maladies infectieuses persistantes et émergentes en Afrique de l’Ouest [Dakar, Sénégal] (Equipe 3 - VITROME), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), The study was funded by Institut Pasteur de Dakar and Institute de Recherche pour le Developpement de Dakar., Institut Pasteur [Paris] (IP), Collège Doctoral, and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)
Subjects: Microbiology (medical), medicine.medical_specialty, Plasmodium, 030231 tropical medicine, Plasmodium falciparum, Psychological intervention, malaria, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Asymptomatic, 03 medical and health sciences, 0302 clinical medicine, Environmental health, Malaria elimination, Epidemiology, parasitic diseases, medicine, Prevalence, Humans, asymptomatic, 030212 general & internal medicine, Malaria, Falciparum, Asymptomatic Infections, interventions, business.industry, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, medicine.disease, 3. Good health, Infectious Diseases, Carriage, Cross-Sectional Studies, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Scale (social sciences), Georeference, [SDV.IMM]Life Sciences [q-bio]/Immunology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, clinical malaria, medicine.symptom, business, Malaria, clustering
Abstract: Background A detailed understanding of the contribution of the asymptomatic Plasmodium reservoir to the occurrence of clinical malaria at individual and community levels is needed to guide effective elimination interventions. This study investigated the relationship between asymptomatic Plasmodium falciparum carriage and subsequent clinical malaria episodes in the Dielmo and Ndiop villages in Senegal. Methods The study used a total of 2792 venous and capillary blood samples obtained from asymptomatic individuals and clinical malaria datasets collected from 2013 to 2016. Mapping, spatial clustering of infections, and risk analysis were performed using georeferenced households. Results High incidences of clinical malaria episodes were observed to occur predominantly in households of asymptomatic P falciparum carriers. A statistically significant association was found between asymptomatic carriage in a household and subsequent episode of clinical malaria occurring in that household for each individual year (P values were 0.0017, 6 × 10–5, 0.005, and 0.008 for the years 2013, 2014, 2015, and 2016 respectively) and the combined years (P = 8.5 × 10–8), which was not found at the individual level. In both villages, no significant patterns of spatial clustering of P falciparum clinical cases were found, but there was a higher risk of clinical episodes Conclusion The findings provide strong epidemiological evidence linking the asymptomatic P falciparum reservoir to clinical malaria episodes at household scale in Dielmo and Ndiop villagers. This argues for a likely success of a mass testing and treatment intervention to move towards the elimination of malaria in the villages of Dielmo and Ndiop.
Published: 2021
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20. Mathematical modelling of Banana Black Sigatoka Disease with delay and Seasonality

Author: Franklin Agouanet, Jean Jules Tewa, Israël Tankam-Chedjou, Remy Magloire Etoua, Département de Mathématiques Université de Yaoundé 1 = Department of Mathematics [Yaoundé, Cameroon], Université de Yaoundé I, Laboratoire International de Recherche en Informatique et Mathématiques Appliquées (LIRIMA), Université de Yaoundé I-Université Badji Mokhtar - Annaba [Annaba] (UBMA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Joseph Ki-Zerbo [Ouagadougou] (UJZK)-Université d'Antananarivo-Université Gaston Bergé Sénégal-Centre National de la Recherche Scientifique et Technologique (CNRST), National Advanced School of Engineering (University of Yaounde I), Centre d’Excellence en Technologies de l’Information et de la Communication (CETIC asbl), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU), EPITAG, Université de Yaoundé I-Université Badji Mokhtar Annaba (UBMA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Joseph Ki-Zerbo [Ouagadougou] (UJZK)-Université d'Antananarivo-Université Gaston Bergé Sénégal-Centre National de la Recherche Scientifique et Technologique (CNRST), Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord]), Department of Mathematics [Yaoundé], and University of Yaoundé [Cameroun]
Subjects: 0106 biological sciences, 0303 health sciences, Black sigatoka, biology, Applied Mathematics, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, food and beverages, Seasonality, biology.organism_classification, medicine.disease, 01 natural sciences, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 03 medical and health sciences, Modeling and Simulation, Statistics, medicine, Mycosphaerella, Basic reproduction number, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany, Mathematics
Abstract: Black Sigatoka Disease, also called Black Leaf Streak Disease (BLSD), is caused by the fungus Mycosphaerella fijiensis and is arguably one of the most important pathogens affecting the banana and plantain industries. Theoretical results on its dynamics are rare, even though theoretical descriptions of epidemics of plant diseases are valuable steps toward their efficient management. In this paper, we propose a mathematical model describing the dynamics of BLSD on banana or plantain leaves within a whole field of plants. The model consists of a system of periodic non-autonomous differential equations with a time delay that accounts for the time of incubation ofM. fijiensis’ spores. We compute the basic reproduction number of the disease and show that it does not depend on the time delay, meaning that the persistence of BLSD would not qualitatively change even if the incubation period of the pathogen is perturbed. We derive local and global long-term dynamics of the disease and provide numerical simulations to illustrate our results.
Published: 2021
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21. Antimicrobial Resistance in Africa—How to Relieve the Burden on Family Farmers

Author: Marion Bordier, Barbara Wieland, Flavie Goutard, François Roger, Ekta Patel, Alexis Delabouglise, Muriel Figuié, Marisa Peyre, Charlotte Dehays, Alexandre Hobeika, Christian Lienhardt, Arshnee Moodley, Christian Ducrot, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Montpellier Interdisciplinary center on Sustainable Agri-food systems (Social and nutritional sciences) (UMR MoISA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), International Livestock Research Institute [CGIAR, Nairobi] (ILRI), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Département Systèmes Biologiques (Cirad-BIOS), Laboratoire National d'Elevage et de Recherches Vétérinaires [Dakar] (LNERV), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Faculty of Veterinary Medicine [Kasetsart University, Thaïlande], Kasetsart University (KU)-Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Université Eduardo Mondlane, University of Copenhagen = Københavns Universitet (UCPH), LESUR, Hélène, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), and University of Copenhagen = Københavns Universitet (KU)
Subjects: antibiotic resistance, Epidemiology, [SDV]Life Sciences [q-bio], Psychological intervention, Infectious and parasitic diseases, RC109-216, 0403 veterinary science, Anti-Infective Agents, Antimicrobial Resistance in Africa—How to Relieve the Burden on Family Farmers, Socioeconomics, 2. Zero hunger, 0303 health sciences, Farmers, Enquête, Qualitative interviews, 1. No poverty, 04 agricultural and veterinary sciences, Antimicrobial, 3. Good health, Anti-Bacterial Agents, [SDV] Life Sciences [q-bio], Infectious Diseases, Perspective, Medicine, Public Health, Microbiology (medical), medicine.medical_specialty, Veterinary Drugs, agriculture familiale, 040301 veterinary sciences, Exploitation agricole familiale, farms animals, L75 - Pharmacologie et toxicologie, family farmers, Agent pathogène, antimicrobials, 03 medical and health sciences, Antibiotic resistance, Drug Resistance, Bacterial, medicine, Animals, Humans, antimicrobial resistance, 030304 developmental biology, business.industry, Public health, L01 - Élevage - Considérations générales, Antimicrobial use, Agriculture, Africa, Business, Antimicrobien, Résistance aux antimicrobiens
Abstract: International audience; Although currently available data indicate that Africa has the lowest usage of antimicrobials in animals in the world (adjusted by animal biomass), data show a high prevalence of antimicrobial resistance in foodborne pathogens isolated from animals and animal products. Apart from the lack of solid data on antimicrobial use in many countries in Africa, diff erent hypotheses could explain this situation. Qualitative interviews of farmers show a lack of knowledge and uninformed use of antimicrobials. Considering the development of animal farming to meet an increasing demand for proteins, this defi ciency represents a serious public health issue. We advocate for policies that consider the specifi c challenges faced by family farmers in Africa, to simultaneously improve access to veterinary drugs while strengthening the regulation of their use. We propose a global approach targeting the agri-food system, off ering innovative social and technical interventions on antimicrobial usage, adapted to family farmers.
Published: 2021
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22. Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde

Author: Bram Vrancken, Cecílio Mendes Pires, Jorge Noel Barreto, Ousmane Faye, Maryam Diarra, Silvânia Da Veiga Leal, Mamadou Diop, Ibrahima Socé Fall, Carolina Cardoso da Silva Leite Gomes, Fabiana Gámbaro-Roglia, Mariano Salazar Castellon, Maria de Lourdes Monteiro, Amadou A. Sall, Philippe Lemey, Déborah Delaune, Linete Fernandes, António Lima Moreira, Matthieu Prot, Oumar Faye, Jessica Ramos, Frédéric Lemoine, Cheikh Loucoubar, Sebastian Lequime, Tomás Valdez, Maria da Luz Lima Mendonça, Laurence Ma, Sandra Tavarez, Oumar Ndiaye, Etienne Simon-Loriere, Anavaj Sakuntabhai, Edward C. Holmes, Gamou Fall, Maria do Céu Teixeira, Maria Filomena Tavares, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Ministry of Health [Cape Verde], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Institut Pasteur [Paris] (IP), World Health Organisation (WHO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Université Paris-Sud - Paris 11 (UP11), Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Génétique fonctionnelle des maladies infectieuses - Functional Genetics of Infectious Diseases, The University of Sydney, This work was supported by Institut Pasteur de Dakar. P.L. received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725422-ReservoirDOCS) and by the Wellcome Trust through project 206298/Z/17/Z. S.L. and B.V. are supported by the Fonds Wetenschappelijk Onderzoek (Belgium). E.S.-L. received funding from the INCEPTION program (Investissements d’Avenir grant ANR-16-CONV-0005) and Institut Pasteur. F.G.-R. is part of the Pasteur-Paris University International doctoral program, BioSPC doctoral school. E.C.H. is funded by an Australian Research Council Australian Laureate Fellowship (FL170100022)., We thank 2 anonymous reviewers whose suggestions helped to improve this manuscript, ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 0725422(2007), Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Biomédicale des Armées (IRBA), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: Microcephaly, vector-borne infections, lcsh:Medicine, serology, phylogeography, Zika virus, Disease Outbreaks, 0302 clinical medicine, Epidemiology, Cabo Verde, epidemiologic studies, microcephaly, 030212 general & internal medicine, Cape Verde, biology, Zika Virus Infection, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Africa, Western, Infectious Diseases, Geography, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Synopsis, epidemiology, Brazil, Microbiology (medical), medicine.medical_specialty, Lineage (genetic), 030231 tropical medicine, Asian lineage, Virus, Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde, lcsh:Infectious and parasitic diseases, Cape verde, 03 medical and health sciences, West Africa, genomics, medicine, Humans, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, viruses, Western Africa, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], outbreak, lcsh:R, Outbreak, Zika Virus, biology.organism_classification, medicine.disease, Virology, Phylogeography, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, disease outbreaks, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: During 2015-2016, Cape Verde, an island nation off the coast of West Africa, experienced a Zika virus (ZIKV) outbreak involving 7,580 suspected Zika cases and 18 microcephaly cases. Analysis of the complete genomes of 3 ZIKV isolates from the outbreak indicated the strain was of the Asian (not African) lineage. The Cape Verde ZIKV sequences formed a distinct monophylogenetic group and possessed 1-2 (T659A, I756V) unique amino acid changes in the envelope protein. Phylogeographic and serologic evidence support earlier introduction of this lineage into Cape Verde, possibly from northeast Brazil, between June 2014 and August 2015, suggesting cryptic circulation of the virus before the initial wave of cases were detected in October 2015. These findings underscore the utility of genomic-scale epidemiology for outbreak investigations. ispartof: EMERGING INFECTIOUS DISEASES vol:26 issue:6 pages:1084-1090 ispartof: location:United States status: published
Published: 2020
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23. Projected Number of People With Onchocerciasis-Loiasis Coinfection in Africa, 1995 to 2025

Author: Luc E. Coffeng, Belen Pedrique, Samuel Wanji, Afework H. Tekle, Jan H. F. Remme, Natalie V. S. Vinkeles Melchers, Sébastien D. S. Pion, Honorat G. M. Zouré, Wilma A. Stolk, Michel Boussinesq, Public Health, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Drugs for Neglected Diseases Initiative, Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), University of Buéa, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), and Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)
Subjects: river blindness, law.invention, Loa, ONCHOSIM, 0302 clinical medicine, Ivermectin, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, law, 030212 general & internal medicine, Articles and Commentaries, mass drug administration, biology, Coinfection, onchocerciasis, Loa loa, 3. Good health, AcademicSubjects/MED00290, Infectious Diseases, Transmission (mechanics), RAPLOA, APOC, medicine.drug, Markov transition, Microbiology (medical), eye worm, 030231 tropical medicine, ivermectin, 03 medical and health sciences, Environmental health, parasitic diseases, medicine, Animals, Humans, stochastic, Mass drug administration, model, business.industry, REMO, Central africa, loiasis, biology.organism_classification, medicine.disease, Onchocerca volvulus, serious adverse events, Africa, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Onchocerciasis, business
Abstract: Background Onchocerciasis elimination through mass drug administration (MDA) is hampered by coendemicity of Loa loa, as people with high L. loa microfilariae (mf) density can develop serious adverse events (SAEs) after ivermectin treatment. We assessed the geographical overlap of onchocerciasis and loiasis prevalence and estimated the number of coinfected individuals at risk of post-ivermectin SAEs in West and Central Africa from 1995 to 2025. Methods Focusing on regions with suspected loiasis transmission in 14 countries, we overlaid precontrol maps of loiasis and onchocerciasis prevalence to calculate precontrol prevalence of coinfection by 5 km2 × 5 km2 pixel, distinguishing different categories of L. loa mf intensity. Using statistical and mathematical models, we predicted prevalence of both infections and coinfection for 2015 and 2025, accounting for the impact of MDA with ivermectin. Results The number of people infected with onchocerciasis was predicted to decline from almost 19 million in 1995 to 4 million in 2025. Of these, 137 000 people were estimated to also have L. loa hypermicrofilaremia (≥20 000 L. loa mf/mL) in 1995, declining to 31 000 in 2025. In 2025, 92.8% of coinfected cases with loiasis hypermicrofilaremia are predicted to live in hypoendemic areas currently not targeted for MDA. Conclusions Loiasis coinfection is a major concern for onchocerciasis elimination in Africa. We predict that under current strategies, at least 31 000 coinfected people still require treatment for onchocerciasis in 2025 while being at risk of SAEs, justifying continued efforts in research and development for safer drugs and control strategies., Onchocerciasis elimination using mass drug administration with ivermectin is jeopardized in areas with Loa loa coendemicity. We estimate the number of people at risk of serious adverse events due to ivermectin in onchocerciasis– loiasis coendemic areas in Africa between 1995 and 2025.
Published: 2020
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24. Mobile community-based active case-finding for tuberculosis among older populations in rural Cambodia

Author: S. Scholtissen, Maryline Bonnet, Cathy Hewison, Jean-Philippe Dousset, O Camelique, Mathieu Bastard, Institut de Recherche pour le Développement (IRD [France-Sud]), Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), and Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)
Subjects: Male, Rural Population, Pulmonary and Respiratory Medicine, medicine.medical_specialty, Tuberculosis, diagnosis, 030231 tropical medicine, Antitubercular Agents, detection, elderly, Asymptomatic, Older population, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Active tb, Internal medicine, medicine, Humans, Mass Screening, 030212 general & internal medicine, Tuberculosis, Pulmonary, Aged, Retrospective Studies, business.industry, screening, Retrospective cohort study, Middle Aged, Patient Acceptance of Health Care, medicine.disease, chest X-ray, 3. Good health, Infectious Diseases, Treatment success, Cough, Case finding, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, medicine.symptom, Cambodia, business, Rural population
Abstract: OBJECTIVE: To systematically screen older rural populations in Cambodia for tuberculosis (TB) and develop an effective active case-finding (ACF) model for this TB high-risk group.DESIGN: A retrospective study using routinely collected programmatic data on community-based ACF among people aged ≥55 years using TB symptoms and systematic chest radiography (CXR) screening, followed by Xpert® MTB/RIF testing for participants with positive screening results and TB culture for certain Xpert-negative specimens.RESULTS: Of 22 101 participants included in the analysis, 7469 (33.8%) were screening-positive and 5960 (27.0%) underwent Xpert testing. Pulmonary TB was identified in 482 (2.2%) individuals: 288 (1.3%) were bacteriologically confirmed (253 using Xpert, 35 using culture) and 194 (0.9%) were clinically diagnosed. Eighty-seven people needed to be screened in order to diagnose one Xpert-positive case. Among the Xpert-positive cases, only 31.6% (80/253) reported cough ≥2 weeks, and 39.9% (101/253) were asymptomatic but had a CXR suggestive of active TB. Treatment uptake was 97.3% (469/482), and treatment success was 88.0% (424/482).CONCLUSIONS: Community-based ACF was effective in detecting and successfully treating older TB patients, most of whom might otherwise have remained undiagnosed. Mobile CXR appears to be crucial in identifying a high number of asymptomatic, bacteriologically confirmed cases.
Published: 2019
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25. Epidemiology and antifungal susceptibility testing of non-albicans Candida species colonizing mucosae of HIV-infected patients in Yaoundé (Cameroon)

Author: Sébastien Bertout, Rufin M.K. Toghueo, F. Fekam Boyom, Laurence Lachaud, Charles Kouanfack, A.K. Nana, L. Tadjou, I.F. Kenfack, Thierry Kammalac Ngouana, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Université de Yaoundé I, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Hôpital Central de Yaoundé [Yaoundé], Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Génétique et évolution des maladies infectieuses (GEMI), and CCSD, Accord Elsevier
Subjects: Adult, Male, MALDI-TOF, Antifungal, medicine.medical_specialty, Susceptibility testing, Antifungal Agents, Adolescent, Itraconazole, medicine.drug_class, Candida glabrata, HIV Infections, Microbial Sensitivity Tests, Biology, Microbiology, Young Adult, 03 medical and health sciences, Drug Resistance, Fungal, Amphotericin B, Epidemiology, medicine, Humans, Candida tropicalis, Cameroon, Non-albicans Candida species, Fluconazole, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Aged, Candida, 0303 health sciences, 030306 microbiology, Middle Aged, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Yeast, 3. Good health, Colonisation, Infectious Diseases, HIV-patients, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Female, medicine.drug
Abstract: International audience; Non-albicans Candida (NAC) species have emerged as potent pathogenic yeasts among HIV-infected patients. Authors evaluated the epidemiology and antifungal susceptibility testing of non-albicansCandida species colonizing Yaoundé (capital of the Republic of Cameroon, Central Africa) HIV-infected patients. The mucosal specimens were collected and submitted to the mycological diagnosis. Yeast isolates were identified by the Matrix Assisted Laser Desorption Ionisation - Time of Flight Mass Spectrometry (MALDI-TOF MS). The antifungal susceptibility testing was achieved by the CLSI-M27 protocols, and the interpretation of clinical break points (CBPs) and epidemiological cutoff values were in accordance with the CLSI-M60 and M59 recommendations. Four hundred and two patients were recruited and 1218 samples collected. The colonisation frequency was 24.1% and 304 yeasts isolated. Yeast isolates were 113 (37.2%) C. albicans, 2 (0.7%) C. africana and 172 (56.6%) NAC isolates. The NAC isolates were grouped into 13 species including C. krusei (18.1%), C. glabrata (10.9%), C. tropicalis (8.5%) and C. parapsilosis (5.9%) as the major ones. All the isolates appeared to be wild-type for amphotericin B and itraconazole. One (1/33) isolate of C. glabrata was resistant to fluconazole. C. arapsilosis isolates appeared all susceptible to fluconazole. C. tropicalis isolates presented 50% (13/26) resistance to fluconazole. The achieved results bring out new insights about epidemiology of NAC species in Cameroon. The results also highlight the resistance of NAC species to current antifungal drugs.
Published: 2019
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26. Risk assessment of using off‐label morphine sulfate in a population‐based retrospective cohort of opioid‐dependent patients

Author: Nicolas Authier, Denis Ardid, Jessica Delorme, Hélène Peyrière, Georges Brousse, Célian Bertin, Chouki Chenaf, Marie Riquelme, Alain Eschalier, Neuro-Dol (Neuro-Dol), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Faculté de Médecine - Clermont-Ferrand, Université d'Auvergne - Clermont-Ferrand I (UdA), Pharmacologie fondamentale et clinique de la douleur, Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Pôle de biologie médicale et d'anatomie pathologique, CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Neuro-Dol - Clermont Auvergne (Neuro-Dol), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire Gabriel Montpied, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), and Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)
Subjects: Male, medicine.medical_specialty, [SDV]Life Sciences [q-bio], Risk Assessment, 030226 pharmacology & pharmacy, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Opiate Substitution Treatment, medicine, Humans, Pharmacology (medical), 030212 general & internal medicine, ComputingMilieux_MISCELLANEOUS, Retrospective Studies, Pharmacology, Morphine, business.industry, Incidence (epidemiology), Retrospective cohort study, Opioid use disorder, Off-Label Use, Original Articles, Opioid-Related Disorders, medicine.disease, Confidence interval, Buprenorphine, 3. Good health, Analgesics, Opioid, Opioid, Cohort, business, Delivery of Health Care, Methadone, medicine.drug
Abstract: AIMS: Several addictovigilance studies have described the off‐label use of morphine sulfate (MS) for nonchronic pain in opioid use disorder (OUD) patients as an alternative to conventional opioid substitution treatments (OSTs). This study primarily sought to compare the incidence of unintentional opioid‐related overdose in the year following the prescription initiation in off‐label MS users, compared to OST‐maintained patients. METHODS: Sequential cohorts of OUD patients who were regularly dispensed MS, buprenorphine, or methadone, between 1 April 2012 and 31 December 2014, were retrospectively identified using the French nationwide healthcare data system. The incidence of overdoses, deaths, doctor shopping, and complications of a viral, bacterial or thrombotic nature, was compared using the Cox regression method. RESULTS: Overall, 1075, 20 834 and 9778 OUD patients without chronic‐pain were included in the MS, buprenorphine, and methadone cohorts, respectively. Overdose incidence was 3.8 (P
Published: 2019
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27. Combined Sexual Behavioral Profiles in HIV-Seronegative Men Who have Sex with Men in West Africa (CohMSM ANRS 12324-Expertise France)

Author: Pierre-Julien, Coulaud, Luis, Sagaon-Teyssier, Mohamed, Mimi, Bakridine, M'madi Mrenda, Gwenaëlle, Maradan, Marion, Mora, Michel, Bourrelly, Bintou Dembélé, Keita, Abdoul Aziz, Keita, Camille, Anoma, Stéphane-Alain, Babo Yoro, Ter Tiero Elias, Dah, Christian, Coulibaly, Ephrem, Mensah, Selom, Agbomadji, Adeline, Bernier, Clotilde, Couderc, Christian, Laurent, Bruno, Spire, Claver Anoumou Yaotsè, Dagnra, Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), ARCAD-SIDA [Bamako, Mali], Espace Confiance [Abidjan, Côte d’Ivoire], Association African Solidarité [Ouagadougou, Burkina Faso], Centre Muraz [Bobo-Dioulasso, Burkina Faso], Espoir Vie Togo [Lomé, Togo], Coalition PLUS [Pantin, France], Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), CohMSM Study Group: Clotilde Couderc, Bruno Granouillac, Suzanne Izard, Christian Laurent, Laura March, Martine Peeters, Laetitia Serrano, Cyril Berenger, Michel Bourrelly, Pierre-Julien Coulaud, Gwenaëlle Maradan, Bakri M'madi Mrenda, Marion Mora, Enzo Parisi, Luis Sagaon-Teyssier, Bruno Spire, Adeline Bernier, Paméla Palvadeau, Daniela Rojas Castro, Drissa Camara, Oumar Cisse, Alou Coulibaly, Bintou Dembele Keita, Fodié Diallo, Mahamadou Diarra, Mady Gadjigo, Abdoul Aziz Keita, Kader Maiga, Aly Ouologuem, Fodé Traore, Niamkey Thomas Aka, Camille Anoma, Stéphane-Alain Babo Yoro, Noufo Hamed Coulibaly, Rachelle Kotchi, Patrick Kouabenan, Malan Jean-Baptiste Kouame, Kpassou Julien Lokrou, Frédéric Dibi N'Guessan, Xavier Anglaret, Jean-Marie Masumbuko, Maxime Oga, Christian Coulibaly, Ter Tiero Elias Dah, Ousseni Ilboudo, Joseph Ouedraogo, Mamadou Ouedraogo, Elisabeth Thio, Juste Rodrigue Toure, Abdoulazziz Traore, Issa Traore, Fiffou Yougbare, Nicolas Meda, Kouakou Kokouvi Selom Agbomadji, Richard Mawuényégan Kouamivi Agboyibor, Messan Attiogbe, Aléda Mawuli Badjassim, Agbégnigan Lorette Ekon, Anouwarsadat Kokouba, Ephrem Mensah, Diimiln Joseph Strauss Tablissi, Kossi Jeff Yaka, Claver Anoumou Yaotsè Dagnra, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), and Dupuis, Christine
Subjects: Male, Sexual behavior, [SDV]Life Sciences [q-bio], HIV risk, Human immunodeficiency virus (HIV), HIV Infections, Human sexuality, medicine.disease_cause, West africa, Men who have sex with men, Cohort Studies, Sexual and Gender Minorities, 0302 clinical medicine, MESH: Sexual Partners, 030212 general & internal medicine, 10. No inequality, MESH: Cohort Studies, General Psychology, virus diseases, MESH: HIV Infections, 3. Good health, [SDV] Life Sciences [q-bio], MESH: Sexual and Gender Minorities, Africa, Western, Sexual Partners, MESH: Risk-Taking, MESH: Young Adult, Cohort, Sexual orientation, 0305 other medical science, Psychology, Adult, medicine.medical_specialty, MESH: Homosexuality, Male, Young Adult, 03 medical and health sciences, Risk-Taking, Arts and Humanities (miscellaneous), Identity, MESH: Africa, Western, West Africa, medicine, Humans, MSM, Homosexuality, Male, MESH: Humans, 030505 public health, Public health, MESH: Adult, MESH: Male, Demography
Abstract: International audience; Understanding the dynamics of HIV infection in men who have sex with men (MSM) can help improve efficiency in existing prevention strategies. We aimed to identify and describe the sexual behaviors of MSM most at risk of HIV infection in West Africa. HIV-negative MSM were provided a quarterly preventive follow-up package in the community-based cohort CohMSM. They completed face-to-face sociobehavioral questionnaires every 6 months. This sub-study on 520 participants used a baseline, 6-, 12- and 18-month data cluster analysis to categorize two profiles (high risk [HRE] and moderate risk [MRE] of exposure to HIV) based on three risky sexual practices over the previous 6 months. HRE-MSM (61%) were more engaged in receptive practices, had a higher proportion of inconsistent condom use during anal sex, and reported more sexual partners than MRE-MSM (39%). The proportion of HIV seroconversions observed during the first 18 months of follow-up using sexual behavioral profiles (92% are HRE-MSM) was higher than using the three risky sexual practices separately. Factors associated with the HRE-MSM profile were being younger (18-21 years), reporting stigma, and having had no female partner while being attracted only to men. Our findings suggest that in order to identify MSM most at risk of HIV infection, several risky sexual practices need to be evaluated in a combined approach. Prevention programs should pay particular attention to younger MSM, and implement activities addressing questions of MSM identity and stigma in order to reduce the dynamic of HIV infection in Western African MSM.
Published: 2019
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28. Increased Prevalence of Neurocognitive Impairment in Aging People Living With Human Immunodeficiency Virus: The ANRS EP58 HAND 55–70 Study

Author: Pascale Leclercq, Christian Geny, Jonathan Dubois, Mélanie Simony, Claudine Barbuat, Sabrina Eymard-Duvernay, Alain Makinson, Louis Bernard, Matteo Vassallo, Anna Ozguler, Jacques Reynes, Marie Zins, Dominique Costagliola, Claudine Berr, Eric Thouvenot, Olivia Zaegel-Faucher, Berr, Claudine, Infrastructures - La cohorte CONSTANCES - Infrastructure épidémiologique ouverte pour la recherche et la surveillance - - CONSTANCES2011 - ANR-11-INBS-0002 - INBS - VALID, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Neuropsychiatrie : recherche épidémiologique et clinique (PSNREC), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Unité des Maladies Infectieuses [CHU Grenoble-Alpes], Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Fédération d’Infectiologie Multidisciplinaire de l’Arc Alpin [CHU Grenoble-Alpes], Service d'Immuno-hématologie clinique [Hôpital Sainte Marguerite - APHM], Assistance Publique - Hôpitaux de Marseille (APHM)-Hôpital Sainte-Marguerite [CHU - APHM] (Hôpitaux Sud ), Service de Médecine Interne et Maladies Infectieuses [Tours], Service de Médecine Interne [CH Cannes], Centre Hospitalier de Cannes (CH Cannes), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Hôpital Gui de Chauliac, Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Sorbonne Université (SU), Cohortes épidémiologiques en population (CONSTANCES), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université Paris Cité (UPCité), ANRS France Recherche Nord & sud Sida-hiv hépatites, This study was supported by France Recherche Nord & Sud Sida-VIH Hépatites (ANRS). A donation was also given by Merck & Co. The CONSTANCES Cohort Study is an Infrastructure nationale en Biologie et Santé and benefits from a grant from ANR (ANR-11-INBS-0002). This study was sponsored by Inserm-ANRS (Institut national de la santé et de la recherché médicale - France Recherche Nord & Sud Sida-VIH Hépatites)., ANR-11-INBS-0002,CONSTANCES,La cohorte CONSTANCES - Infrastructure épidémiologique ouverte pour la recherche et la surveillance(2011), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université de Paris (UP), Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), Neuropsychiatrie : recherche épidémiologique et clinique, Université Grenoble Alpes (UGA), Centre Hospitalier Régional Universitaire de Nîmes (CHRU Nîmes), UMS011 Cohortes épidémiologiques en population (CONSTANCES), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), ANR-11-INBS-0002/11-INBS-0002,CONSTANCES,La cohorte CONSTANCES - Infrastructure épidémiologique ouverte pour la recherche et la surveillance(2011), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Hôpital Gui de Chauliac [CHU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), and Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)
Subjects: Male, Microbiology (medical), medicine.medical_specialty, Lymphocyte, HIV Infections, HAND, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Prevalence, neurocognitive impairment, medicine, Humans, 030212 general & internal medicine, Aged, business.industry, aging, Confounding, HIV, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, Odds ratio, Middle Aged, Confidence interval, 3. Good health, Clinical trial, Cross-Sectional Studies, Infectious Diseases, medicine.anatomical_structure, Cohort, Female, Frascati criteria, business, Neurocognitive, Viral load, [SDV.NEU.SC] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, 030217 neurology & neurosurgery
Abstract: Background There are limited data on the comparative prevalence of neurocognitive impairment (NCI) in aging people living with human immunodeficiency virus (PLHIV) and people not living with HIV. Methods This was a cross-sectional study of PLHIV randomly matched by age (±4 years), gender, and education with 5 HIV-uninfected individuals from the CONSTANCES cohort. PLHIV were fluent in French and sequentially included during routine outpatient visits if aged 55–70 years, with HIV viral load Results Two hundred PLHIV were matched with 1000 controls. Median age was 62 years, and 85% were men. In PLHIV, the median T-CD4 lymphocyte level was 650 cells/µL, and median nadir T-CD4 lymphocyte level was 176 cells/µL. NCI was found in 71 (35.5%) PLHIV and in 242 (24.2%) controls (odds ratio [OR], 1.74; 95% confidence interval [CI], 1.25, 2.41). After adjusting for confounders, HIV remained significantly associated with NCI (OR, 1.50; 95% CI, 1.04, 2.16). Adjusted results were similar with NCI defined by MNC (ORMNC, 2.95; 95% CI, 1.13, 3.50) or −1.5 SD (OR−1.5, 2.24; 95% CI, 1.39, 3.62). Conclusions In this matched study of aging individuals, HIV was significantly associated with an increased risk of NCI after adjusting for major confounders. Results were confirmed with more stringent NCI classifications. Clinical Trials Registration NCT02592174.
Published: 2019
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29. 2018 Ebola virus disease outbreak in Équateur Province, Democratic Republic of the Congo: a retrospective genomic characterisation

Author: Moussa Moïse Diagne, Ousmane Faye, Sophie Duraffour, Shanmuga Sozhamannan, John Kombe, Oumar Faye, Martine Peeters, Daniel Mukadi, Anastasie Mulumba, Nicole Vidal, Maggie L. Bartlett, Eric F. Donaldson, Eric Delaporte, Elisabeth Pukuta, Mariano Sanchez-Lockhart, Patrick Mukadi, Sheila Makiala-Mandanda, Timothy D. Minogue, Mamadou Diop, Amadou A. Sall, Catherine B. Pratt, Jeanette Gonzalez, Amuri Aziza, Justus Nsio, Stephen M. Gross, Placide Mbala-Kingebeni, Steve Ahuka-Mundeke, Stormy Karhemere, Jacques Likofata, Jens H. Kuhn, Felix Mulangu, Nicholas Di Paola, Joseph A. Chitty, Jean Jacques Muyembe-Tamfum, Ahidjo Ayouba, Michael R. Wiley, Gary P. Schroth, Katie Caviness, Aaron Aruna, Gustavo Palacios, Institut National de Recherche Biomédicale [Kinshasa] (INRB), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Institut de Recherche pour le Développement (IRD [France-Sud]), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Montpellier (UM), University of Nebraska Medical Center, University of Nebraska System, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Aiello, Mélisande, Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], viruses, 030106 microbiology, Genomics, ZMapp, Biology, medicine.disease_cause, Antiviral Agents, Genome, Disease Outbreaks, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, medicine, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Ebola Vaccines, Retrospective Studies, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Ebola virus, Phylogenetic tree, Outbreak, Hemorrhagic Fever, Ebola, Biological product, Ebolavirus, Virology, 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, Infectious Diseases, GenBank, Democratic Republic of the Congo, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, medicine.drug
Abstract: Summary Background The 2018 Ebola virus disease (EVD) outbreak in Equateur Province, Democratic Republic of the Congo, began on May 8, and was declared over on July 24; it resulted in 54 documented cases and 33 deaths. We did a retrospective genomic characterisation of the outbreak and assessed potential therapeutic agents and vaccine (medical countermeasures). Methods We used target-enrichment sequencing to produce Ebola virus genomes from samples obtained in the 2018 Equateur Province outbreak. Combining these genomes with genomes associated with known outbreaks from GenBank, we constructed a maximum-likelihood phylogenetic tree. In-silico analyses were used to assess potential mismatches between the outbreak strain and the probes and primers of diagnostic assays and the antigenic sites of the experimental rVSVΔG-ZEBOV-GP vaccine and therapeutics. An in-vitro flow cytometry assay was used to assess the binding capability of the individual components of the monoclonal antibody cocktail ZMapp. Findings A targeted sequencing approach produced 16 near-complete genomes. Phylogenetic analysis of these genomes and 1011 genomes from GenBank revealed a distinct cluster, confirming a new Ebola virus variant, for which we propose the name “Tumba”. This new variant appears to have evolved at a slower rate than other Ebola virus variants (0·69 × 10−3 substitutions per site per year with “Tumba” vs 1·06 × 10−3 substitutions per site per year without “Tumba”). We found few sequence mismatches in the assessed assay target regions and antigenic sites. We identified nine amino acid changes in the Ebola virus surface glycoprotein, of which one resulted in reduced binding of the 13C6 antibody within the ZMapp cocktail. Interpretation Retrospectively, we show the feasibility of using genomics to rapidly characterise a new Ebola virus variant within the timeframe of an outbreak. Phylogenetic analysis provides further indications that these variants are evolving at differing rates. Rapid in-silico analyses can direct in-vitro experiments to quickly assess medical countermeasures. Funding Defense Biological Product Assurance Office .
Published: 2019
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30. Actualisation des recommandations françaises de traitement du pemphigus

Author: Catherine Prost-Squarcioni, Olivier Dereure, Vivien Hébert, C. Le Roux-Villet, Fabienne Jouen, E. Le Bidre, M-P Konstantinou, Frédéric Caux, Nadège Cordel, L Jelti, Gaëlle Quéreux, Catherine Picard-Dahan, J. Plée, Christophe Bedane, Michel D'Incan, Denis Jullien, M-A Viguier, Sophie Duvert-Lehembre, Bruno Sassolas, Marina Alexandre, I Bourgault Villada, E. Tancrede-Bohin, Pascal Joly, J-D Bouaziz, Saskia Ingen-Housz-Oro, M-S Doutre, Sébastien Debarbieux, M-A Richard, Emmanuel Delaporte, B. Mellottee, P. Bernard, Service de dermatologie [Avicenne], Université Paris 13 (UP13)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Matrice extracellulaire et dynamique cellulaire - UMR 7369 (MEDyC), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay, Pathogénèse et contrôle des infections chroniques (PCCI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Service de dermatologie [Nantes], Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes), Service de dermatologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Service de Dermatologie [Rouen], Hôpital Charles Nicolle [Rouen]-CHU Rouen, Normandie Université (NU)-Normandie Université (NU), Fonctionnement et évolution des systèmes écologiques (FESE), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Institut Laue-Langevin (ILL), Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), CHU Clermont-Ferrand, Laboratoire de Chimie Industrielle, École Nationale d'Ingénieurs de Sfax | National School of Engineers of Sfax (ENIS), CHU Bordeaux [Bordeaux], CHU Pointe-à-Pitre/Abymes [Guadeloupe], Hopital de Bohars - CHRU Brest (CHU - BREST ), Hôpital Robert Debré, CRCM, Université Paris7, Assistance Publique - Hôpitaux de Paris, Physiopathologie et biothérapies des maladies inflammatoires et autoimmunes, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), ArcelorMittal Maizières Research SA, ArcelorMittal, Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM ), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Hôpital Charles Nicolle [Rouen], École normale supérieure - Paris (ENS Paris), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), ILL, Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Hôpital Charles Nicolle [Rouen], Normandie Université (NU)-Normandie Université (NU)-CHU Rouen, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])
Subjects: medicine.medical_specialty, business.industry, MEDLINE, [SDV.CAN]Life Sciences [q-bio]/Cancer, Dermatology, medicine.disease, 030207 dermatology & venereal diseases, 03 medical and health sciences, Pemphigus, 0302 clinical medicine, 030220 oncology & carcinogenesis, Severity of illness, medicine, Intensive care medicine, business, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019
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31. A Study ofTrichomonas vaginalisInfection and Correlates in Women with Vaginal Discharge Referred at Fann Teaching Hospital in Senegal

Author: Khadime Sylla, Lamine Dia, Thérèse Dieng, Doudou Sow, Babacar Faye, Ahmet Y. Sow, Roger Tine, Rougyatou Ka, Khardiata Diallo, Souleye Lelo, Cheikh Tidiane Ndour, Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), École Supérieure Polytechnique de Dakar (ESP), Laboratoire de Parasitologie, Dakar, Sénégal, and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)
Subjects: Vaginal discharge, medicine.medical_specialty, Article Subject, 030231 tropical medicine, Prevalence, Disease, medicine.disease_cause, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Epidemiology, Medicine, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030212 general & internal medicine, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Trichomoniasis, business.industry, Obstetrics, Vaginal flora, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Infectious Diseases, medicine.anatomical_structure, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Vagina, Parasitology, Trichomonas vaginalis, medicine.symptom, business, Research Article
Abstract: Introduction. Trichomoniasis is nowadays the most prevalent non-viral sexually transmitted infection in the world. In Senegal, the epidemiology of trichomoniasis is not well known. The current study aimed at assessing the prevalence and factors associated withT. vaginalisinfection among women with vaginal discharge.Methods. A retrospective analysis of laboratory records from patients referred at the Fann Teaching Hospital in Dakar, Senegal, for vaginal discharge was carried out. The study covered the period from 2006 to 2011. For each participating woman, a vaginal swab was collected and a wet mount smear performed immediately. Optic microscopic examination with 40x magnification was done to detectT. vaginalisand assess biological modifications such as presence of epithelial cells, white blood cells, and red blood cells. A gram stained smear was also performed and examined under oil immersion (100x magnification) to assess the vaginal flora.Results. Overall, 3893 women were enrolled with a mean age at 31.2 ± 10 years. The prevalence of Trichomoniasis represented 4.8%, 95%CI(3.1-5.7) and it was lower among women less than 30 years (4.1%), while divorced women more likely to be infected compared to married and single women (aOR:2.1, 95%CI (1.2-3.7)). Trichomoniasis was associated with abnormal vaginal flora such as type III (aOR:2.6, 95%CI(1.5-4.4)) and type IV (aOR:3.3, 95%CI(2.1-5.3)). In addition, patients with erythrocytes excretion were more likely to be infected byT. vaginalis(aOR:2.8, 95%CI(1.9-3.9).Conclusion.Trichomonas vaginalisremains prevalent among sexually active women. Strategies aiming at improving disease awareness in these high-risk groups are needed to improve trichomoniasis prevention but extensive epidemiological data are still needed for a better understanding of the disease transmission dynamic.
Published: 2019
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32. Genotype Diversity and Spread of White Spot Syndrome Virus (WSSV) in Madagascar (2012–2016)

Author: Voahangy Rasolofo, Iony Manitra Razanajatovo, Alexandra Bastaraud, Lydia Rabetafika, Alain Moïse Onihary, Jean-Michel Heraud, Laboratoire d'hygiène des aliments et de l'environnement [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université d'Antananarivo, Unité de Virologie [Antananarivo, Madagascar] (IPM), Département de virologie - Virology Department [Dakar], Institut Pasteur de Dakar, Direction scientifique [Antananarivo, Madagascar], and A.M.O. was supported though Girard’s fellowship undergraduate program from the Institut Pasteur de Madagascar.
Subjects: Veterinary medicine, viruses, genotype, White spot syndrome, Biology, Microbiology, Penaeus monodon, Shrimp farming, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genotype, Madagascar, 14. Life underwater, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Macrobrachium rosenbergii, Outbreak, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 04 agricultural and veterinary sciences, Metapenaeus monoceros, biology.organism_classification, White Spot Syndrome Virus (WSSV), QR1-502, Shrimp, virology, Infectious Diseases, aquaculture, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 040102 fisheries, 0401 agriculture, forestry, and fisheries, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract: White Spot Disease (WSD) caused by the White Spot Syndrome Virus (WSSV) is the most devastating viral disease threatening the shrimp culture industry worldwide, including Madagascar. WDS was first reported on the island in 2012, however, little is known about the circulation of the virus and its genetic diversity. Our study aimed at describing the molecular diversity and the spread of WSSV in the populations of Madagascan crustaceans. Farmed and wild shrimps were collected from various locations in Madagascar from 2012 to 2016 and were tested for WSSV. Amplicons from positive specimens targeting five molecular markers (ORF75, ORF94, ORF125, VR14/15 and VR23/24) were sequenced for genotyping characterizations. Four genotypes were found in Madagascar. The type-I genotype was observed in the south-west of Madagascar in April 2012, causing a disastrous epidemic, then spread to the North-West coast. Type-II strains were detected in October 2012 causing an outbreak in another Penaeus monodon farm. In 2014 and 2015, types II and III were observed in shrimp farms. Finally, in 2016, types II and IV were found in wild species including Fenneropenaeus indicus, Metapenaeus monoceros, Marsupenaeus japonicus and Macrobrachium rosenbergii. Considering the economic importance of the shrimp industry for Madagascar, our study highlights the need to maintain WSSV surveillance to quickly take appropriate countermeasures in case of outbreak and to sustain this industry.
Published: 2021
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33. Physicochemical factors affecting the diversity and abundance of Afrotropical Culicoides species in larval habitats in Senegal

Author: Jérémy Bouyer, Claire Garros, Mamadou Ciss, Moussa Fall, Thierry Baldet, Mame Thierno Bakhoum, Geoffrey Gimonneau, Momar Talla Seck, Assane Gueye Fall, Laboratoire National d'Elevage et de Recherches Vétérinaires [Dakar] (LNERV), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Université de Bordeaux (UB)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), M.T.B. was granted by the Islamic Development Bank (Ref. 36/11207330, and File No. 66/SEN/P34) . Field missions were was funded by the project 'Integrated Vector Management: innovating to improve control and reduce environmental impacts' of Institut Carnot Sante Animale (ICSA) excellence network (http://www6.jouy.inra.fr/gabi/LePartenariat/LInstitutCarnotSanteAnimaleICSA) . M.T.B. would like to thank Adja Rokhaya DIARRA and Georgette Rokhy Ndiaye, ISRALNERV, BP 2057, Dakar, Senegal.
Subjects: 0301 basic medicine, Niayes area, Salinity, [SDV]Life Sciences [q-bio], Expérimentation in vivo, Ceratopogonidae, Soil, Salinité, 0302 clinical medicine, Abundance (ecology), Larva, pH, Ecology, Culicoides oxystoma, Culicoides, Facteur du milieu, Hydrogen-Ion Concentration, 030108 mycology & parasitology, Substrate (marine biology), Expérimentation in vitro, Senegal, Vecteur de maladie, Substrat de culture, Infectious Diseases, Habitat, L20 - Écologie animale, Veterinary (miscellaneous), 030231 tropical medicine, Larval habitat, Biology, 03 medical and health sciences, Animals, Ecosystem, Propriété physicochimique, fungi, biology.organism_classification, Physicochemical parameters, Fèces, Insect Science, Vector (epidemiology), Écologie animale, Parasitology, African horse sickness
Abstract: International audience; Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) are the biological vectors of arboviruses of global importance in animal health. We characterized the physicochemical parameters that determine the density and composition of the main Culicoides species of veterinary interest in larval habitats of the Niayes region of Senegal. For this purpose, we combined larval and substrate sampling in the field in different habitat types with adult emergence and physicochemical analyses in the laboratory. Three major habitat types were identified, conditioning the predominant species of Culicoides and pH and the amount of organic matter were positively correlated with the abundance of larvae and emerging Culicoides, as opposed to salinity. The diversity of emerging Culicoides was positively correlated with pH while it was negatively correlated with salinity. Culicoides distinctipennis was the predominant species in the larval habitat group of freshwater lake edges. In the larval habitat group of pond and puddle edges, C. oxystoma and C. nivosus were predominant; both species were again most abundant in the larval habitat group of saltwater lake edges. These variabilities in physicochemical parameters support the distribution of different Culicoides species in different habitat groups. These results make it possible to implement effective, selective and environmental-friendly control measures but also to improve current models for estimating the abundance of adult vector populations at a local scale.
Published: 2021
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34. Risk Prediction of Cognitive Decline after Stroke

Author: Youssef Hbid, Abdel Douiri, Majed Obaid, Charles D.A. Wolfe, Marion Fahey, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU), Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Cadi Ayyad [Marrakech] (UCA), King‘s College London, Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord]), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)
Subjects: Male, Time Factors, medicine.medical_treatment, [SDV]Life Sciences [q-bio], Cognitive decline, Neuropsychological Tests, 0302 clinical medicine, Cognition, Risk Factors, London, Registries, 10. No inequality, Stroke, Aged, 80 and over, education.field_of_study, Rehabilitation, medicine.diagnostic_test, Linear model, Stroke Rehabilitation, Middle Aged, case mix, Mental Status and Dementia Tests, Prognosis, Cohort, Female, Cardiology and Cardiovascular Medicine, mixed-effects model, medicine.medical_specialty, clinical prediction, Population, Risk Assessment, rehabilitation, 03 medical and health sciences, recovery, Case mix index, Predictive Value of Tests, Internal medicine, medicine, Humans, Cognitive Dysfunction, education, Aged, Ischemic Stroke, Mini–Mental State Examination, business.industry, Post-stroke, medicine.disease, monitoring, Surgery, Neurology (clinical), business, 030217 neurology & neurosurgery
Abstract: Background and purpose Cognitive decline is one of the major outcomes after stroke. We have developed and evaluated a risk predictive tool of post-stroke cognitive decline and assessed its clinical utility. Methods In this population-based cohort, 4,783 patients with first-ever stroke from the South London Stroke Register (1995-2010) were included in developing the model. Cognitive impairment was measured using the Mini Mental State Examination (cut off 24/30) and the Abbreviated Mental Test (cut off 8/10) at 3-months and yearly thereafter. A penalised mixed-effects linear model was developed and temporal-validated in a new cohort consisted of 1,718 stroke register participants recruited from (2011-2018). Prediction errors on discrimination and calibration were assessed. The clinical utility of the model was evaluated using prognostic accuracy measurements and decision curve analysis. Results The overall predictive model showed good accuracy, with root mean squared error of 0.12 and R2 of 73%. Good prognostic accuracy for predicting severe cognitive decline was observed AUC: (88%, 95% CI [85-90]), (89.6%, 95% CI [86-92]), (87%, 95% CI [85-91]) at 3 months, one and 5 years respectively. Average predicted recovery patterns were analysed by age, stroke subtype, Glasgow-coma scale, and left-stroke and showed variability. Decision curve analysis showed an increased clinical benefit, particularly at threshold probabilities of above 15% for predictive risk of cognitive impairment. Conclusions The derived prognostic model seems to accurately screen the risk of post-stroke cognitive decline. Such prediction could support the development of more tailored management evaluations and identify groups for further study and future trials.
Published: 2021
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35. The COVID-19 Pandemic and the Need for an Integrated and Equitable Approach: An International Expert Consensus Paper

Author: Sergio Pillon, Mariella Catalano, Benjamin Brenner, Zsolt Pecsvarady, Ismail Elalamy, Joseph Lewis, Jean-Claude Wautrecht, D. Olinic, Vincent Maréchal, Mouna Sassi, Isabelle Mahé, Anna Falanga, Nusrat Jabeen, Charles A. Carter, Mary-Paula Colgan, Alexander Makatsariya, Alfonso Tafur, Kasse Aa, Tazi Mezalek Zoubida, Meletios-Athanasios Dimopoulos, Michèle Sabbah, Darko Antic, Yiannis Theodorou, Alex C. Spyropoulos, Vladimir Chekhonin, Meganathan Kannan, Katalin Farkas, Peter Klein-Wegel, Job Harenberg, P Massamba Mbaye, Joseph Gligorov, Manuel Monreal Bosch, Grigoris T. Gerotziafas, Pier Luigi Antignani, Hikmat Abdel-Razeq, James D. Douketis, Gerit Schernthaner, Petros Agathaggelou, Ali T. Taher, Jawed Fareed, Essam Abo Elnazar, Irina Panovska-Stavridis, Patrick Van Dreden, Fabio Leivano, Gerry Fowkes, Fakiha Siddiqui, Mark A. Ligocki, Tishya Indran, Kostantinos Konstantinidis, Bulent Kantarcioglu, Jin Shiomura, Bahare Fazeli, Chryssa Papageorgiou, Yongquan Gu, Anny Slama-Schwok, Eduardo Ramacciotti, Zenguo Zhai, Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), CHU Tenon [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Università degli Studi di Milano = University of Milan (UNIMI), Centre d'Immunologie et des Maladies Infectieuses (CIMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sechenov First Moscow State Medical University, Campbell University [Buies Creek, NC, USA] (CU), University of Karachi, Heidelberg University, Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Loyola University [Chicago], Cyprus Institute (CyI), University of Belgrade [Belgrade], Nuova Villa Claudia [Rome, Italy] (NVC), Universidad Católica San Antonio de Murcia (UCAM), Rambam Health Care Campus [Haifa, Israel], Technion - Israel Institute of Technology [Haifa], Ministry of Health of the Russian Federation (MHRF), St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Trinity College Dublin, National and Kapodistrian University of Athens (NKUA), McMaster University [Hamilton, Ontario], Firestone Institute for Respiratory Health [Hamilton, ON, Canada] (FIRH), Ministry of Health [Saudi Arabia], Szent Imre Hospital [Budapest, Hungary] (SIH), Mashhad University of Medical Sciences, University of Edinburgh, Capital University of Medical Sciences [Beijing] (CUMS), Hôpitaux Universitaires de l'Est Parisien [Paris] (HUEP), Monash Medical Centre [Clayton, Australia], Central University of Tamil Nadu [Thiruvarur, India] (CUTN), Central University of Tamil Nadu (CUTN), Okmeydani Training and Research Hospital [Istanbul, Turkey] (OTRH), Centre International de Cancérologie de Dakar [Dakar, Senegal] (CICD), Aristotle University of Thessaloniki, University Hospital Southampton NHS Foundation Trust, Université Virtuelle du Sénégal [Dakar, Senegal] (UVS), Innovations thérapeutiques en hémostase (IThEM - U1140), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University Clinic of Hematology [Skopje, Republic of North Macedonia] (UCH), University of Medicine and Pharmacy [Cluj-Napoca, Romania] (UMP), Service d'Anesthésie réanimation [CHU Tenon], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Flor Ferenc Teaching Hospital [Kistarcsa, Hungary] (2FTH), San Camillo Forlanini Hospital [Rome], Loyola University Medical Center (LUMC), Science Valley Research Institute [São Paulo, Brazil] (SVRI), King Hussein Cancer Center [Amman, Jordan] (KH2C), CHU Fattouma Bourguiba [Monastir] (HFB), Medizinische Universität Wien = Medical University of Vienna, Nobelpharma Co. Ltd. [Tokyo, Japan], Hôpital Erasme [Bruxelles] (ULB), Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), North Shore University Cardiologists [Skokie, Illinois, USA] (NSUC), American University of Beirut Faculty of Medicine and Medical Center (AUB), Klinikum Ernst von Bergmann [Potsdam, Germany] (KEVB), Peking University [Beijing], Chinese Academy of Medical Sciences [Beijing, China] (CAMS), Peking Union Medical College [Beijing, China], Université Mohammed V de Rabat [Agdal] (UM5), Scientific Reviewer Committee: Gregory Y H Lip, Michael Makris, Sam Schulman, Wolfgang Siess, Christian Weber, Sabbah, Michèle, Centre de Recherche Saint-Antoine (CR Saint-Antoine), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Saint-Antoine [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University of Milan, Centre d'Immunologie et de Maladies Infectieuses (CIMI), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), and University of Mohammed V
Subjects: medicine.medical_specialty, Telemedicine, Economic growth, COVID-19 Vaccines, Population, Psychological intervention, Disease, 030204 cardiovascular system & hematology, Risk Assessment, Herd immunity, 03 medical and health sciences, COVID-19 Testing, 0302 clinical medicine, Consensus Paper, Pandemic, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030212 general & internal medicine, Disease management (health), education, Pandemics, thrombosis, education.field_of_study, SARS-CoV-2, Immunization Programs, pandemic, Public health, COVID-19, Disease Management, health care systems, Hematology, 3. Good health, Public Health, Business
Abstract: Background One year after the declaration of the coronavirus disease 2019 (COVID-19) pandemic by the World Health Organization (WHO) and despite the implementation of mandatory physical barriers and social distancing, humanity remains challenged by a long-lasting and devastating public health crisis. Management Non-pharmacological interventions (NPIs) are efficient mitigation strategies. The success of these NPIs is dependent on the approval and commitment of the population. The launch of a mass vaccination program in many countries in late December 2020 with mRNA vaccines, adenovirus-based vaccines, and inactivated virus vaccines has generated hope for the end of the pandemic. Current Issues The continuous appearance of new pathogenic viral strains and the ability of vaccines to prevent infection and transmission raise important concerns as we try to achieve community immunity against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and its variants. The need of a second and even third generation of vaccines has already been acknowledged by the WHO and governments. Perspectives There is a critical and urgent need for a balanced and integrated strategy for the management of the COVID-19 outbreaks organized on three axes: (1) Prevention of the SARS-CoV-2 infection, (2) Detection and early diagnosis of patients at risk of disease worsening, and (3) Anticipation of medical care (PDA). Conclusion The “PDA strategy” integrated into state policy for the support and expansion of health systems and introduction of digital organizations (i.e., telemedicine, e-Health, artificial intelligence, and machine-learning technology) is of major importance for the preservation of citizens' health and life world-wide.
Published: 2021
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36. Bulinus senegalensis and Bulinus umbilicatus Snail Infestations by the Schistosoma haematobium Group in Niakhar, Senegal

Author: Bruno Senghor, Mbacké Sembène, Babacar Faye, Doudou Sow, Ndiaw Goumballa, Souleymane Doucoure, Cheikh Sokhna, Coralie L'Ollivier, Stéphane Ranque, Papa Mouhamadou Gaye, Philippe Parola, Maladies infectieuses persistantes et émergentes en Afrique de l’Ouest [Dakar, Sénégal] (Equipe 3 - VITROME), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Faculté des Sciences et Techniques (FST), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)
Subjects: 0301 basic medicine, Veterinary medicine, Bulinus senegalensis, Snail, medicine.disease_cause, 0302 clinical medicine, S. bovis, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Dra1, Immunology and Allergy, Bulinus umbilicatus, Schistosoma haematobium, education.field_of_study, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, 3. Good health, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Medicine, Microbiology (medical), Wet season, 030231 tropical medicine, Population, Schistosomiasis, Article, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, biology.animal, schistosomiasis, Infestation, parasitic diseases, medicine, Bulinus, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, education, Molecular Biology, General Immunology and Microbiology, Schistosoma haematobium-group, Niakhar, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, RD-PCR
Abstract: Thorough knowledge of the dynamics of Bulinus spp. infestation could help to control the spread of schistosomiasis. This study describes the spatio-temporal dynamics of B. senegalensis and B. umbilicatus infestation by the Schistosoma haematobium group of blood flukes in Niakhar, Senegal. Molecular identification of the S. haematobium group was performed by real-time PCR, targeting the Dra 1 gene in 810 samples of Bulinus spp. collected during the schistosomiasis transmission season in 2013. In addition to Dra 1 PCR, a rapid diagnostic-PCR was performed on a sub-group of 43 snails to discriminate S. haematobium, S. bovis, and S. mattheei. Out of 810 snails, 236 (29.1%) were positive for Dra 1 based on the PCR, including 96.2% and 3.8% of B. senegalensis and B. umbilicatus, respectively. Among the sub-group, 16 samples were confirmed to be S. haematobium while one was identified as a mixture of S. haematobium and S. bovis. Snails infestations were detected in all villages sampled and infestation rates ranged from 15.38% to 42.11%. The prevalence of infestation was higher in the north (33.47%) compared to the south (25.74%). Snail populations infestations appear early in the rainy season, with a peak in the middle of the season, and then a decline towards the end of the rainy season. Molecular techniques showed, for the first time, the presence of S. bovis in the Bulinus spp. population of Niakhar. The heterogeneity of snail infestations at the village level must be taken into account in mass treatment strategies. Further studies should help to improve the characterizations of the schistosome population.
Published: 2021
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37. Hydroxychloroquine and Azithromycin Treatment of Hospitalized Patients Infected with SARS-CoV-2 in Senegal from March to October 2020

Author: Ndongo Dia, D. Ka, Khardiata Diallo Mbaye, Billo Tall, Viviane Marie Pierre Cisse Diallo, N A Lakhe, Inès Vigan-Womas, Moussa Seydi, Daouda Thioub, Ousmane Faye, Cheikh Tidiane Diagne, Pape Samba Ba, Amadou Moustapha Ndoye, Margarite Diatta, Fatoumata Diene Sarr, Philippe Dubrous, Aboubakar Sidikh Badiane, Abdoulaye Seck, Aboubacry Gaye, Cheikh Talla, Ndèye Maguette Fall, Moustapha Diop, Mamadou Cisse, Louise Fortes, Mamadou Diop, Cheikh Loucoubar, Amadou A. Sall, Mamadou Aliou Barry, Fabien Taieb, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), CHNU Fann, Hôpital Principal de Dakar, Centre Hospitalier National Dalal Jamm (CHNDJ), UFR-Santé Thiès, Hôpital pour Enfants de Diamniadio, and This research was funded by the Institut Pasteur de Dakar and Welcome Trust Grant 221012/Z/20/Z.
Subjects: medicine.medical_specialty, hydroxychloroquine, Hospitalized patients, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Discharged alive, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 030204 cardiovascular system & hematology, Azithromycin, Article, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, 030212 general & internal medicine, Patient discharge, azithromycin, treatment, business.industry, SARS-CoV-2, Hydroxychloroquine, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, Case management, Senegal, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Medicine, [SDV.IMM]Life Sciences [q-bio]/Immunology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Clinical risk factor, medicine.drug
Abstract: International audience; As of today, little data is available on COVID-19 in African countries, where the case management relied mainly on a treatment by association between hydroxychloroquine (HCQ) and azithromycin (AZM). This study aimed to understand the main clinical outcomes of COVID-19 hospitalized patients in Senegal from March to October 20202. We described the clinical characteristics of patients and analysed clinical status (alive and discharged versus hospitalized or died) at 15 days after Isolation and Treatment Centres (ITC) admission among adult patients who received HCQ plus AZM and those who did not receive this combination. A total of 926 patients were included in this analysis. Six hundred seventy-four (674) (72.8%) patients received a combination of HCQ and AZM. Results showed that the proportion of patient discharge at D15 was significantly higher for patients receiving HCQ plus AZM (OR: 1.63, IC 95% (1.09–2.43)). Factors associated with a lower proportion of patients discharged alive were: age ≥ 60 years (OR: 0.55, IC 95% (0.36–0.83)), having of at least one pre-existing disorder (OR: 0.61, IC 95% (0.42–0.90)), and a high clinical risk at admission following NEWS score (OR: 0.49, IC 95% (0.28–0.83)). Few side effects were reported including 2 cases of cardiac rhythmic disorders in the HCQ and AZM group versus 13 in without HCQ + AZM. An improvement of clinical status at 15 days was found for patients exposed to HCQ plus AZM combination
Published: 2021
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38. External quality assessment of Rift Valley fever diagnosis in countries at risk of the disease: African, Indian Ocean and Middle-East regions

Author: Denis Nyakilinga, Soufien Sghaier, Khalil Zro, Nicolas Keck, Catherine Cetre-Sossah, Modou Moustapha Lo, Sara Acha, Fatiha El Mellouli, Thabisile Tshabalala, Ahmed Bezeid El Mamy, Abdulwahed Mohammed Alrizqi, Maman Moutari Souley, Claudia Filippone, Baratang A. Lubisi, Jean-Michel Heraud, Nadera Bouayed, Marthin Dakouo, Sitty-Bahyat Chamassy, Kareem Abdelfattah Abdelwahab Mohammed, Hanane Khallouki, Ghizlane Sebbar, Haladou Gagara, Aurélie Pédarrieu, Jelly Chang’a, Abdallah Traoré, M. Diop, Hafsa Madani, Gilda Grard, Laurenco Mapaco, Yahya Barry, Abdou Achiraffi, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Régional d'Analyses et de Recherches de Casablanca (LRARC), Office National de Sécurité Sanitaire des Produits Alimentaires [Maroc] (ONSSA), Biopharma [Rabat, Maroc], Université de Tunis El Manar (UTM), Institut National de la Médecine Vétérinaire [Mohammadia, Algérie] (INMV), Laboratoire National d'Elevage et de Recherches Vétérinaires [Dakar] (LNERV), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Office National de Recherche et de Développement de l’Elevage (ONARDEL), Laboratoire Central Vétérinaire [Bamako, Mali], Laboratoire Central de l’Elevage [Niamey, Niger] (LABOCEL), Mozambique Institute of Agricultural Research (IIAM), Tanzania Veterinary Laboratory Agency [Dar es Salaam, Tanzania] (TVLA), ARC-Onderstepoort Veterinary Research [Onderstepoort, South Africa] (ARC-OVR), Unité de Virologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Laboratoire vétérinaire et d’analyses départemental [Mayotte, France] (LVAD976), Laboratoire Départemental Vétérinaire de l'Hérault, Conseil Général de l'Hérault, Centre National de Référence (CNR) des Arbovirus - Laboratoire coordonnateur : Equipe Résidente de Recherche d'Infectiologie Tropicale (ERRIT), Institut de Recherche Biomédicale des Armées Hôpital d’Instruction des Armées Laveran, Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Jazan Veterinary Diagnostic Laboratory [Jizan, Kingdom of Saudi Arabia], This study was partly funded by the SURE project, Préfecture de la Réunion, INTERREG FEDER TROI 2015-2017 in the framework of the DP One Health Indian Ocean., We are grateful to Annelise Tran for her help producing the map illustrating the countries that took part in the PT, and to Denise Bastron for registering the participants and sending the panels to the participating laboratories. The authors would like also to thank the veterinarians (CoopADEM, Food, Agriculture and Forestry Directorate (DAAF, Direction de l’Alimentation, de l’Agriculture et de la Forêt) for their assistance in obtaining the blood samples., Agricultural Research Institute of Mozambique, and Heraud, Jean-Michel
Subjects: RNA viruses, Research Facilities, Endemic Diseases, Quality Assurance, Health Care, Rift Valley Fever, Epidemiology, Antibodies, Viral, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Serology, Geographical Locations, 0302 clinical medicine, Risk Factors, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Zoonoses, Bunyaviruses, Rift Valley fever, Indian Ocean, Pathology and laboratory medicine, Neglected tropical diseases, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, biology, Medical microbiology, Veterinary Diagnostics, 3. Good health, Geography, Veterinary Diseases, Preparedness, S50 - Santé humaine, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Infectious diseases, Medicine, Livestock, Pathogens, Research Laboratories, Research Article, Medical conditions, Veterinary Medicine, Science, 030231 tropical medicine, Enzyme-Linked Immunosorbent Assay, Viral diseases, Research and Analysis Methods, Arbovirus, Microbiology, 03 medical and health sciences, Middle East, Environmental health, External quality assessment, medicine, Animals, Humans, Serologic Tests, 030304 developmental biology, Medicine and health sciences, Biology and life sciences, business.industry, Tropical diseases, Organisms, Viral pathogens, Outbreak, Reproducibility of Results, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, medicine.disease, biology.organism_classification, Rift Valley fever virus, Microbial pathogens, Phlebovirus, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Medical Risk Factors, Immunoglobulin G, People and Places, Africa, Veterinary Science, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Laboratories, Government Laboratories
Abstract: Rift Valley fever virus (RVFV), an arbovirus belonging to the Phlebovirus genus of the Phenuiviridae family, causes the zoonotic and mosquito-borne RVF. The virus, which primarily affects livestock (ruminants and camels) and humans, is at the origin of recent major outbreaks across the African continent (Mauritania, Libya, Sudan), and in the South-Western Indian Ocean (SWIO) islands (Mayotte). In order to be better prepared for upcoming outbreaks, to predict its introduction in RVFV unscathed countries, and to run efficient surveillance programmes, the priority is harmonising and improving the diagnostic capacity of endemic countries and/or countries considered to be at risk of RVF. A serological inter-laboratory proficiency test (PT) was implemented to assess the capacity of veterinary laboratories to detect antibodies against RVFV. A total of 18 laboratories in 13 countries in the Middle East, North Africa, South Africa, and the Indian Ocean participated in the initiative. Two commercial kits and two in-house serological assays for the detection of RVFV specific IgG antibodies were tested. Sixteen of the 18 participating laboratories (88.9%) used commercial kits, the analytical performance of test sensitivity and specificity based on the seroneutralisation test considered as the reference was 100%. The results obtained by the laboratories which used the in-house assay were correct in only one of the two criteria (either sensitivity or specificity). In conclusion, most of the laboratories performed well in detecting RVFV specific IgG antibodies and can therefore be considered to be prepared. Three laboratories in three countries need to improve their detection capacities. Our study demonstrates the importance of conducting regular proficiency tests to evaluate the level of preparedness of countries and of building a network of competent laboratories in terms of laboratory diagnosis to better face future emerging diseases in emergency conditions.
Published: 2021
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39. Diversification, selective sweep, and body size in the invasive Palearctic alfalfa weevil infected with Wolbachia

Author: Khadim Kébé, Julien Haran, Ahmed H. El-Heneidy, Midori Tuda, Jiri Skuhrovec, Shun Ichiro Iwase, Katsura Morimoto, Ehsan Sanaei, Ottó Merkl, Attila Podlussány, Naomichi Tsuji, Kyushu University, École Supérieure Polytechnique de Dakar (ESP), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Crop research institute, School of Biological Sciences [Brisbane], University of Queensland [Brisbane], Graduate School of Bioresource and Bioenvironmental Sciences [Fukuoka], Hungarian Natural History Museum (Magyar Természettudományi Múzeum), Plant Protection Research Institute (PPRI), Funding was provided by Japan Society for the Promotion of Science (Grant Nos. JP23405008, JP25430194, JP26304016, JP17H04612, JP18H02207 and JP19K06840), Kyushu University (Interdisciplinary Programs in Education and Projects in Research Development (25412)) and Ministerstvo Zemědělství (Grant No. RO0418)., Kyushu University [Fukuoka], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Nonsynonymous substitution, Male, Population genetics, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, 01 natural sciences, Génétique des populations, Body Size, Clade, Phylogeny, Lutte antiravageur, Ravageur des plantes, Multidisciplinary, biology, Ecology, Weevil, Hypera postica, Mitochondria, Europe, Phylogenetics, Phylogeography, Medicine, Wolbachia, Female, Cytoplasmic incompatibility, Asia, Evolution, Science, Zoology, 010603 evolutionary biology, Microbiology, Article, 03 medical and health sciences, Variation génétique, Animals, Genetic diversity, Bacteria, ved/biology, Genetic Variation, biology.organism_classification, H10 - Ravageurs des plantes, 030104 developmental biology, Haplotypes, Weevils, Selective sweep, Introduced Species
Abstract: The alfalfa weevil Hypera postica, native to the Western Palearctic, is an invasive legume pest with two divergent mitochondrial clades in its invading regions, the Western clade and the Eastern/Egyptian clade. However, knowledge regarding the native populations is limited. The Western clade is infected with the endosymbiotic bacteria Wolbachia that cause cytoplasmic incompatibility in host weevils. Our aim was to elucidate the spatial genetic structure of this insect and the effect of Wolbachia on its population diversity. We analyzed two mitochondrial and two nuclear genes of the weevil from its native ranges. The Western clade was distributed in western/central Europe, whereas the Eastern/Egyptian clade was distributed from the Mediterranean basin to central Asia. Intermediate mitotypes were found from the Balkans to central Asia. Most Western clade individuals in western Europe were infected with an identical Wolbachia strain. Mitochondrial genetic diversity of the infected individuals was minimal. The infected clades demonstrated a higher nonsynonymous/synonymous substitution rate ratio than the uninfected clades, suggesting a higher fixation of nonsynonymous mutations due to a selective sweep by Wolbachia. Trans-Mediterranean and within-European dispersal routes were supported. We suggest that the ancestral populations diversified by geographic isolation due to glaciations and that the diversity was reduced in the west by a recent Wolbachia-driven sweep(s). The intermediate clade exhibited a body size and host plant that differed from the other clades. Pros and cons of the possible use of infected-clade males to control uninfected populations are discussed.
Published: 2021
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40. An open-label randomized controlled trial of the effect of lopinavir/ritonavir, lopinavir/ritonavir plus IFN-β-1a and hydroxychloroquine in hospitalized patients with COVID-19

Author: Lionel Piroth, Bruno Mourvillier, Joy Mootien, François-Xavier Lescure, Emmanuel Faure, S. Gallien, Dominique Costagliola, Jean-Christophe Richard, Noemie Mercier, Florent Wallet, Yazdan Yazdanpanah, Marion Noret, Claire Andrejak, Jean-Philippe Lanoix, Julien Poissy, Johan Courjon, Saad Nseir, François Danion, Violaine Tolsma, Alain Makinson, Odile Launay, Raphaël Clere-Jehl, Bruno Lina, Drifa Belhadi, Valérie Pourcher, Antoine Kimmoun, Karine Lacombe, Juliette Saillard, Maude Bouscambert-Duchamp, Stéphane Jauréguiberry, Charles Burdet, Toni Alfaiate, Olivier Epaulard, Minh Patrick Lê, Gilles Peytavin, Elisabeth Botelho-Nevers, Thérèse Staub, Guillaume Martin-Blondel, Alpha Diallo, Lila Bouadma, Aline Dechanet, François Goehringer, Florence Ader, Nathan Peiffer-Smadja, Jean-Christophe Navellou, Christelle Delmas, Rostane Gaci, Kevin Bouiller, Maya Hites, André Cabié, Jean Reuter, Sylvie Leroy, Axelle Dupont, François Raffi, Amandine Gagneux-Brunon, Jean Reignier, Clément Dubost, Hospices Civils de Lyon (HCL), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Services de Maladies Infectieuses et Tropicales [CHU Bichat], AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, National Institute for Health Research [Cambridge, UK], Imperial College London, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CHU Lille, Centre National de Reference des virus des Infections Respiratoires France Sud [HCL, Lyon], Virology and human respiratory Pathologies - Virology and human respiratory Pathologies (VirPath), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Centre d'investigation Clinique [CHU Bichat] - Épidémiologie clinique (CIC 1425), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM), ANRS France Recherche Nord & sud Sida-hiv hépatites, Institut de Santé Publique, Université de Médecine Carol Davila, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre d’Investigation Clinique de Nantes (CIC Nantes), Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre hospitalier universitaire de Nantes (CHU Nantes), Service des Maladies Infectieuses et Tropicales [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Défaillance Cardiovasculaire Aiguë et Chronique (DCAC), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), French-Clinical Research Infrastructure Network - F-CRIN [Paris] (Cardiovascular & Renal Clinical Trialists - CRCT ), Cardiovascular and Renal Clinical Trialists [Vandoeuvre-les-Nancy] (INI-CRCT), Institut Lorrain du Coeur et des Vaisseaux Louis Mathieu [Nancy], Service de Réanimation Médicale [CHRU Nancy], AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Centre National de Référence du Paludisme [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Centre hospitalier universitaire de Nantes (CHU Nantes), Université de Nantes (UN), Les Hôpitaux Universitaires de Strasbourg (HUS), Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), LabEx Transplantex [Strasbourg], Université de Strasbourg (UNISTRA), Nouvel Hôpital Civil de Strasbourg, Fédération Hospitalo-Universitaire (OMICARE), Centre de Recherche d’Immunologie et d’Hématologie [Strasbourg], Fédération de Médecine Translationnelle de Strasbourg (FMTS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Centre Hospitalier Annecy-Genevois [Saint-Julien-en-Genevois], Centre d'Investigation Clinique Antilles-Guyane (CIC - Antilles Guyane), Université des Antilles et de la Guyane (UAG)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -CHU de Fort de France-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Pathogenesis and Control of Chronic and Emerging Infections (PCCEI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université des Antilles (UA)-Etablissement français du don du sang [Montpellier], Etablissement français du don du sang [Montpellier], CHU de la Martinique [Fort de France], Hôpital d'Instruction des Armées Begin, Service de Santé des Armées, Université Paris-Saclay, Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), CB - Centre Borelli - UMR 9010 (CB), Service de Santé des Armées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-Université de Paris (UP), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Centre Hospitalier Universitaire de Nice (CHU Nice), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), FHU OncoAge - Pathologies liées à l’âge [CHU Nice] (OncoAge), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Centre Hospitalier Emile Muller [Mulhouse] (CH E.Muller Mulhouse), Groupe Hospitalier de Territoire Haute Alsace (GHTHA), Centre hospitalier régional Metz-Thionville (CHR Metz-Thionville), Centre Hospitalier Universitaire de Reims (CHU Reims), Université de Reims Champagne-Ardenne (URCA), Université Lille Nord de France (COMUE), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), CIC Cochin Pasteur (CIC 1417), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université de Paris (UP)-Groupe hospitalier Broca-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôtel-Dieu-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Saint-Antoine [AP-HP], Agents infectieux, résistance et chimiothérapie - UR UPJV 4294 (AGIR ), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, Infectious and Tropical Diseases Department [Montpellier], Institut de Recherche pour le Développement (IRD)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM), CIC Montpellier, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-CHU Saint-Eloi-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CHU Toulouse [Toulouse], Physiopathologie et biothérapies des infections muqueuses (GIMAP), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Jean Monnet [Saint-Étienne] (UJM), Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Fédération d’Infectiologie Multidisciplinaire de l’Arc Alpin [CHU Grenoble-Alpes], Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre d'Investigation Clinique 1432 (Dijon) - Epidemiologie Clinique/Essais Cliniques (CIC-EC), Université de Bourgogne (UB)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital de la Croix-Rousse [CHU - HCL], Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA), Centre Hospitalier de Luxembourg [Luxembourg] (CHL), Institut des Agents Infectieux [Lyon] (IAI), Réseau national de recherche clinique en infectiologie (RENARCI), CHU Amiens-Picardie, Université libre de Bruxelles (ULB), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de Recherches sur le Sida et les Hépatites Virales (ANRS), Université de Lorraine (UL), Hôpital Bicêtre, Sorbonne Université-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire [Besançon] (CHRU Besançon), Université des Antilles (UA)-Etablissement français du don du sang [Montpellier]-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU de Fort de France-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française]-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles et de la Guyane (UAG), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Université Côte d'Azur (UCA), Université de Lille, Sorbonne Université, Sorbonne Université-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Sorbonne Université (SU), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université, Département Maladies Infectieuses et Tropicales, Hôpital Universitaire, Montpellier, France, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), CIC Saint Etienne, Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Nord (Saint Etienne), Optimisation thérapeutique en Neuropsychopharmacologie (OPTeN (UMR_S_1144 / U1144)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Hôpital Erasme [Bruxelles] (ULB), Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Département d'Epidemiologie, Biostatistique et Recherche Clinique (DEBRC), Centre National de Référence du Paludisme [CHU Pitié-Salpétrière] (CNRpalu), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de Santé des Armées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-Université Paris Cité (UPCité), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC)-Université Côte d'Azur (UCA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Service de Maladies Infectieuses et Tropicales [CHU Pitié-Salpêtrière], AP-HP, Hôpital Henri-Mondor Albert-Chenevier, Service d'Immunologie Clinique et Maladies Infectieuses 94000 Créteil, France, Université Paris-Est Créteil Val-de-Marne - Faculté de médecine (UPEC Médecine), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôtel-Dieu-Groupe hospitalier Broca-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Services des Maladies Infectieuses et Tropicales [CHU Saint-Antoine], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Saint Eloi (CHRU Montpellier), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Service des maladies infectieuses et tropicales [Toulouse], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse], Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Jean Monnet [Saint-Étienne] (UJM), CHU Grenoble, Université Grenoble Alpes (UGA), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire Chrono-environnement (UMR 6249) (LCE), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service Maladies infectieuses et tropicales [CHU Toulouse], Pôle Inflammation, infection, immunologie et loco-moteur [CHU Toulouse] (Pôle I3LM Toulouse), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Centre d'Investigation Clinique - Epidémiologie Clinique Saint-Etienne (CIC-EC), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC)-Université Sorbonne Paris Nord, Service de Santé des Armées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-Université Paris Cité (UPC), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôtel-Dieu-Groupe hospitalier Broca-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Lopinavir/ritonavir, law.invention, 0302 clinical medicine, Randomized controlled trial, law, immune system diseases, MESH: Antiviral Agents* / therapeutic use, 030212 general & internal medicine, MESH: Treatment Outcome, education.field_of_study, MESH: Middle Aged, virus diseases, Lopinavir, General Medicine, MESH: Lopinavir / therapeutic use, 3. Good health, Infectious Diseases, MESH: Interferon beta-1a / therapeutic use, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Pharmaceutical Preparations, MESH: Hydroxychloroquine / therapeutic use, [SDV.IMM]Life Sciences [q-bio]/Immunology, Original Article, medicine.drug, Hydroxychloroquine, Microbiology (medical), medicine.medical_specialty, 030106 microbiology, Population, Antiviral Agents, 03 medical and health sciences, Interferon β-1a, Internal medicine, medicine, Humans, education, Adverse effect, MESH: COVID-19* / drug therapy, MESH: Drug Combinations, MESH: Humans, business.industry, SARS-CoV-2, Drug Repositioning, Interferon beta-1a, COVID-19, MESH: Adult, MESH: Male, MESH: Ritonavir / therapeutic use, Ritonavir, business, MESH: Female, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; Objectives: We evaluated the clinical, virological and safety outcomes of lopinavir/ritonavir, lopinavir/ritonavir-interferon (IFN)-β-1a, hydroxychloroquine or remdesivir in comparison to standard of care (control) in coronavirus 2019 disease (COVID-19) inpatients requiring oxygen and/or ventilatory support.Methods: We conducted a phase III multicentre, open-label, randomized 1:1:1:1:1, adaptive, controlled trial (DisCoVeRy), an add-on to the Solidarity trial (NCT04315948, EudraCT2020-000936-23). The primary outcome was the clinical status at day 15, measured by the WHO seven-point ordinal scale. Secondary outcomes included quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory specimens and pharmacokinetic and safety analyses. We report the results for the lopinavir/ritonavir-containing arms and for the hydroxychloroquine arm, trials of which were stopped prematurely.Results: The intention-to-treat population included 583 participants-lopinavir/ritonavir (n = 145), lopinavir/ritonavir-IFN-β-1a (n = 145), hydroxychloroquine (n = 145), control (n = 148)-among whom 418 (71.7%) were male, the median age was 63 years (IQR 54-71), and 211 (36.2%) had a severe disease. The day-15 clinical status was not improved with the investigational treatments: lopinavir/ritonavir versus control, adjusted odds ratio (aOR) 0.83, (95% confidence interval (CI) 0.55-1.26, p 0.39), lopinavir/ritonavir-IFN-β-1a versus control, aOR 0.69 (95%CI 0.45-1.04, p 0.08), and hydroxychloroquine versus control, aOR 0.93 (95%CI 0.62-1.41, p 0.75). No significant effect of investigational treatment was observed on SARS-CoV-2 clearance. Trough plasma concentrations of lopinavir and ritonavir were higher than those expected, while those of hydroxychloroquine were those expected with the dosing regimen. The occurrence of serious adverse events was significantly higher in participants allocated to the lopinavir/ritonavir-containing arms.Conclusion: In adults hospitalized for COVID-19, lopinavir/ritonavir, lopinavir/ritonavir-IFN-β-1a and hydroxychloroquine improved neither the clinical status at day 15 nor SARS-CoV-2 clearance in respiratory tract specimens.
Published: 2021
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41. Altered subcutaneous adipose tissue parameters after switching ART-controlled HIV+ patients to raltegravir/maraviroc

Author: Soraya Fellahi, Judith Aron-Wisnewsky, Christine Katlama, Véronique Pelloux, Jean-Philippe Bastard, Jacqueline Capeau, Rohia Alili, Karine Clément, Bruno Fève, Emilie Capel, Edi Prifti, Lambert Assoumou, Centre de Recherche Saint-Antoine (CR Saint-Antoine), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Henri Mondor, Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Nutrition et obésités: approches systémiques (nutriomics) (UMR-S 1269 INSERM - Sorbonne Université), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Service de nutrition [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Centre de Recherche en Nutrition Humaine d'Ile-de-France (CRNH-IDF), Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut de Veille Sanitaire (INVS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Sorbonne Paris Nord-Institut National Agronomique Paris-Grignon (INA P-G)-Sorbonne Université (SU)-CETAF-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service d'Endocrinologie, diabétologie et endocrinologie de la reproduction [CHU Saint-Antoine], CHU Saint-Antoine [AP-HP], Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU), Service des maladies infectieuses et tropicales [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Gestionnaire, Hal Sorbonne Université, Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Nutrition et obésités: approches systémiques (UMR-S 1269) (Nutriomics), Service de Nutrition [CHU Pitié-Salpétrière], Institut E3M [CHU Pitié-Salpêtrière], Institut de Veille Sanitaire (INVS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut National Agronomique Paris-Grignon (INA P-G)-CETAF-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Sorbonne Paris Nord, Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord]), Service de Maladies Infectieuses et Tropicales [CHU Pitié-Salpêtrière], CHU Henri Mondor [Créteil], Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), and Institut de Veille Sanitaire (INVS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut National Agronomique Paris-Grignon (INA P-G)-CETAF-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Sorbonne Paris Nord
Subjects: Male, 0301 basic medicine, medicine.medical_specialty, Anti-HIV Agents, [SDV]Life Sciences [q-bio], medicine.medical_treatment, Immunology, Subcutaneous Fat, Adipose tissue, HIV Infections, Maraviroc, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Insulin resistance, Raltegravir Potassium, Adipocyte, Internal medicine, medicine, Humans, Immunology and Allergy, 030212 general & internal medicine, business.industry, Insulin, Raltegravir, medicine.disease, 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, Infectious Diseases, Endocrinology, Adipose Tissue, chemistry, Adipogenesis, business, Viral load, medicine.drug
Abstract: OBJECTIVE To evaluate the effect on anthropometric, metabolic and adipose tissue parameters of switching ART-controlled persons living with HIV (PLWH) from a protease inhibitor regimen to raltegravir/maraviroc. DESIGN Sub-study of the ANRS157 ROCnRAL study with the investigation of subcutaneous abdominal adipose tissue (SCAT) biopsy at inclusion and study end. METHODS We performed lipoaspiration of paired SCAT samples, histology on fresh/fixed samples and examined the transcriptomic profile analyzed using Illumina microarrays after RNA extraction. Statistical analyses used the Wilcoxon-paired test. RESULTS The patients (n = 8) were mainly male (7/8), aged (mean ± standard error of the mean) 54.9 ± 1.2 years, BMI 26.1 ± 1.2 kg/m2, CD4+ 699 ± 56 cells/mm3, all viral load (VL)
Published: 2021
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42. Serological evidence of West Nile virus infection in human populations and domestic birds in the Northwest of Morocco

Author: M’hammed Sarih, Sayeh Ezzikouri, Moussa Dia, Sylvie Lecollinet, Soukaina Arich, Anna-Bella Failloux, Cécile Beck, Najlaa Assaid, Soumaya Benjelloun, Khadija Akarid, Oumar Faye, Laboratoire de Parasitologie et Maladies Vectorielles [Maroc], Institut Pasteur du Maroc, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université Hassan II [Casablanca] (UH2MC), Laboratoire des Hépatites Virales [Casablanca, Maroc] (LHV), Département de virologie - Virology Department [Dakar], Institut Pasteur de Dakar, Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris], This study was funded by Institut Pasteur of Morocco., École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Institut Pasteur [Paris] (IP)
Subjects: viruses, [SDV]Life Sciences [q-bio], Serological evidence, Antibodies, Viral, medicine.disease_cause, Neutralization, Serology, 0403 veterinary science, 0302 clinical medicine, Seroepidemiologic Studies, Immunology and Allergy, MESH: Animals, virus diseases, MESH: Enzyme-Linked Immunosorbent Assay, 04 agricultural and veterinary sciences, General Medicine, 3. Good health, Morocco, Infectious Diseases, MESH: Birds, Antibody, West Nile virus, Human, 040301 veterinary sciences, 030231 tropical medicine, Immunology, Enzyme-Linked Immunosorbent Assay, Biology, Microbiology, Birds, 03 medical and health sciences, Bird, Culex pipiens, medicine, Animals, Humans, Seroprevalence, MESH: West Nile virus, MESH: West Nile Fever, West Nile Virus Infection, MESH: Humans, MESH: Seroepidemiologic Studies, General Veterinary, biology.organism_classification, Virology, MESH: Morocco, biology.protein, West Nile Fever, Virus neutralization test, MESH: Antibodies, Viral
Abstract: International audience; West Nile virus (WNV) was recently detected in Culex pipiens mosquitoes in Morocco. The aim of this study was to evaluate the seroprevalence of WNV in humans and in domestic birds in two regions of Morocco by the detection of IgG antibodies. Blood samples were obtained from 91 human patients and 92 domestic birds from September to December 2019. All study samples were tested using competitive enzyme-linked immunosorbent assay (cELISA) and WNV neutralization tests (VNT) were performed on positive sera. Of all samples, 4 (4.39 %) humans and 4 (4.34 %) birds were found to be seropositive for flaviviruses by the cELISA test. The VNT revealed that three of the four human samples detected positive by cELISA contained neutralizing antibodies against WNV. Two bird samples were confirmed positive by VNT. These results show a significant seroprevalence of anti-WNV antibodies and therefore suggest the active circulation and exposure of human and bird populations in the northwest of Morocco.
Published: 2021
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43. Mycorrhizal inoculation increases fruit production without disturbance of native arbuscular mycorrhizal community in jujube tree orchards (Senegal)

Author: Amadou Moustapha Bâ, Hervé Sanguin, Aboubacry Kane, Diaminatou Sanogo, Sergio Miana de Faria, Robin Duponnois, Cheikh Ndiaye, Babacar Thioye, Samba Ndao Sylla, Dioumacor Fall, UniLaSalle, Agro-écologie, Hydrogéochimie, Milieux et Ressources (AGHYLE), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Centre National de Recherches Forestières de l’Institut Sénégalais de Recherches Agricoles (CNRF), Brazilian Agricultural Research Corporation (Embrapa), Université des Antilles (UA), Africa-Brazil-France tripartite research project, AIRD, Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ), APGMV, Institut de Recherche pour le Developpement (IRD), Institut Senegalais de Recherches Agricoles (ISRA), French Embassy in Senegal (SCAC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Plant Health Institute of Montpellier (UMR PHIM)
Subjects: 0106 biological sciences, 0301 basic medicine, amélioration des cultures, [SDV]Life Sciences [q-bio], Orchard, F62 - Physiologie végétale - Croissance et développement, Performance de culture, 01 natural sciences, Persistence (computer science), Cultivar, [SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 2. Zero hunger, food and beverages, Ziziphus, Biofertilisant, Horticulture, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Fruit production, General Agricultural and Biological Sciences, F60 - Physiologie et biochimie végétale, Biofertilizer, Cultivars, Mycorhization, Biology, 03 medical and health sciences, Inoculation, F03 - Production et traitement des semences, Variété, Glomeromycota, Arbuscular mycorrhiza [EN], fungi, Sowing, Climat semi-aride, 15. Life on land, biology.organism_classification, Ziziphus mauritiana, 030104 developmental biology, Disturbance (ecology), Fruit tree, 010606 plant biology & botany
Abstract: International audience; Arbuscular mycorrhizal (AM) fungi constitute promising biofertilizers for the deployment of a sustainable agriculture. However, the evaluation of mycorrhizal benefits in the field is poorly documented, notably in fruit tree orchards, and concerns exclusively growth performance and nutrition. Here, we evaluated the persistence of beneficial effects of AM fungal inoculation on two jujube (Ziziphus mauritiana Lam.) cultivars (Tasset and Gola) inoculated in nursery conditions and subsequently transferred in the field until fruit production. The growth-promoting effects on jujube observed in nursery was still maintained 18 months after planting, with significant higher rates of survival and an increase of fruit production for inoculated jujube cultivars. Nevertheless, AM-mediated responses were dependent on cultivar. No major disturbance of native AM fungal community was associated with AM fungal inoculation but a stimulation of AM fungal colonization is probable. The use of mycorrhizal inoculation with the R. irregularis IR27 strain hold promise for the development of efficient jujube orchards under semi-arid conditions.
Published: 2021
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44. Residual Viremia Is Linked to a Specific Immune Activation Profile in HIV-1-Infected Adults Under Efficient Antiretroviral Therapy

Author: Mehwish Younas, Christina Psomas, Christelle Reynes, Renaud Cezar, Lucy Kundura, Pierre Portalès, Corinne Merle, Nadine Atoui, Céline Fernandez, Vincent Le Moing, Claudine Barbuat, Albert Sotto, Robert Sabatier, Audrey Winter, Pascale Fabbro, Thierry Vincent, Jacques Reynes, Pierre Corbeau, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Département Maladies Infectieuses et Tropicales, Hôpital Universitaire, Montpellier, France, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Infectious and Tropical Diseases Department [Montpellier], Institut de Recherche pour le Développement (IRD)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM), Guerineau, Nathalie C., Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Virulence bactérienne et maladies infectieuses (VBMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Institut Desbrest de santé publique (IDESP), Institute of Numerical Mathematics [Moscou] (INM-RAS), Russian Academy of Sciences [Moscow] (RAS), and Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI)
Subjects: CD4-Positive T-Lymphocytes, 0301 basic medicine, [SDV]Life Sciences [q-bio], HIV Infections, CD38, Lymphocyte Activation, endothelium activation, Antiretroviral Therapy, Highly Active, Immunology and Allergy, Medicine, Original Research, Disease Management, Middle Aged, 3. Good health, [SDV] Life Sciences [q-bio], medicine.anatomical_structure, Host-Pathogen Interactions, [SDV.IMM]Life Sciences [q-bio]/Immunology, Disease Susceptibility, low-level viremia, medicine.symptom, Adult, lcsh:Immunologic diseases. Allergy, [SDV.IMM] Life Sciences [q-bio]/Immunology, Endothelium, CD14, T cell, 030106 microbiology, Immunology, Inflammation, Viremia, 03 medical and health sciences, Humans, coagulation, virologic responder, Aged, Duration of Therapy, business.industry, Monocyte, medicine.disease, Cross-Sectional Studies, 030104 developmental biology, inflammation, HIV-1, blip, lcsh:RC581-607, business, Biomarkers, CD8
Abstract: International audience; Chronic immune activation persists in persons living with HIV-1 even though they are aviremic under antiretroviral therapy, and fuels comorbidities. In previous studies, we have revealed that virologic responders present distinct profiles of immune activation, and that one of these profiles is related to microbial translocation. In the present work, we tested in 140 HIV-1-infected adults under efficient treatment for a mean duration of eight years whether low-level viremia might be another cause of immune activation. We observed that the frequency of viremia between 1 and 20 HIV-1 RNA copies/mL (39.5 ± 24.7% versus 21.1 ± 22.5%, p = 0.033) and transient viremia above 20 HIV-1 RNA copies/mL (15.1 ± 16.9% versus 3.3 ± 7.2%, p = 0.005) over the 2 last years was higher in patients with one profile of immune activation, Profile E, than in the other patients. Profile E, which is different from the profile related to microbial translocation with frequent CD38+ CD8+ T cells, is characterized by a high level of CD4+ T cell (cell surface expression of CD38), monocyte (plasma concentration of soluble CD14), and endothelium (plasma concentration of soluble Endothelial Protein C Receptor) activation, whereas the other profiles presented low CD4:CD8 ratio, elevated proportions of central memory CD8+ T cells or HLA-DR+ CD4+ T cells, respectively. Our data reinforce the hypothesis that various etiological factors shape the form of the immune activation in virologic responders, resulting in specific profiles. Given the type of immune activation of Profile E, a potential causal link between low-level viremia and atherosclerosis should be investigated.
Published: 2021
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45. A library preparation optimized for metagenomics of RNA viruses

Author: Biram Biteye, Marc Eloit, Ignace Rakotoarivony, Thomas Balenghien, Claire Garros, Rachid Koual, Patricia Gil, Virginie Dupuy, Serafin Gutierrez, Antoni Exbrayat, Assane Gueye Fall, Grégory L'Ambert, Emmanuel Albina, Etienne Loire, Geoffrey Gimonneau, Albane Marie, Benoit Francés, Julie Reveillaud, Momar Talla Seck, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire National d'Elevage et de Recherches Vétérinaires [Dakar] (LNERV), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Entente Interdépartementale pour la démoustication du littoral méditerranéen (EID), École nationale vétérinaire - Alfort (ENVA), Découverte de pathogènes – Pathogen discovery, Institut Pasteur [Paris] (IP), Centre Collaborateur de l'OIE de Détection et identification chez l’homme des pathogènes animaux émergents et développement d’outils pour leur diagnostic / Collaborating Center for the Detection and identification in humans of emerging animal pathogens and development of tools for their diagnoses (CCOIE-OIECC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé Animale / World Organisation Animal Health [Paris] (OIE), This work was funded by the Direction Générale de l’Alimentation from the French Ministry in charge of agriculture. This work was also funded by the European Union’s Seventh Framework Programme through grants Vmerge (FP7‐613996) and CuliOme (FP7‐291815)., European Project: 291815,EC:FP7:KBBE,FP7-ERANET-2011-RTD,ANIHWA(2012), European Project: 613996,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,VMERGE(2013), European Project: 7247564(1972), Université de Bordeaux (UB)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), École nationale vétérinaire d'Alfort (ENVA), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Organisation Mondiale de la Santé Animale / World Animal Health Information System (OIE-WAHIS)
Subjects: 0106 biological sciences, 0301 basic medicine, Viral metagenomics, [SDV]Life Sciences [q-bio], Banque de gènes, Caulimovirus mosaïque du chou fleur, L73 - Maladies des animaux, 01 natural sciences, Genome, shotgun sequencing, Aedes vexans, Culex pipiens, insects, viromevirus, education.field_of_study, Shotgun sequencing, Virome, [SDV.BA]Life Sciences [q-bio]/Animal biology, Culicoides, PCR, Vecteur de maladie, S50 - Santé humaine, L72 - Organismes nuisibles des animaux, Biotechnology, Population, Computational biology, Genome, Viral, Biology, 010603 evolutionary biology, génomique, 03 medical and health sciences, Virus bluetongue, Genetics, Animals, RNA Viruses, Human virome, education, Ecology, Evolution, Behavior and Systematics, Virus classification, Gene Library, metagenomics, Virus maladie de newcastle, Bacteriome, 030104 developmental biology, Metagenomics, Metagenome, library preparation
Abstract: International audience; Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high-throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. This situation differs from bacteriome studies in which developments in library preparation have largely contributed to the democratisation of metagenomics. Here, we present a library preparation optimized for metagenomics of RNA viruses from insect vectors of viral diseases. The library design allows a simple PCR-based preparation, such as those routinely used in bacterial metabarcoding, that is adapted to shotgun sequencing as required in viral metagenomics. We first optimized our library preparation using mock viral communities and then validated a full metagenomic approach incorporating our preparation in two pilot studies with field-caught insect vectors; one including a comparison with a published metagenomic protocol. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition within a population of a mosquito species. Finally, the sensitivity of our approach was compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught insect vectors. Our approach could facilitate studies on viral communities from animals and the democratization of metagenomics in community ecology of viruses.
Published: 2021
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46. Development of an Illumina-based analysis method to study bradyrhizobial population structure-case study on nitrogen-fixing rhizobia associating with cowpea or peanut

Author: Francis Do Rego, Antoine Le Quéré, Diariatou Niang, Saliou Fall, Seynabou Diop, Noémie Dehaene, Marc Neyra, Tatiana Karsova-Wade, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Commun de Microbiologie IRD/ISRA/UCA, Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), and French Institute of Research for the Development
Subjects: DNA, Bacterial, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Arachis, Nitrogen, Biodiversity, Context (language use), Nitrogen-fixing symbiosis, Applied Microbiology and Biotechnology, Bradyrhizobium, Rhizobia, Crop, 03 medical and health sciences, Bradyrhizobium diversity, RNA, Ribosomal, 16S, Symbiosis, Microbial inoculant, Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Genetic diversity, biology, 030306 microbiology, Vigna, food and beverages, Fabaceae, General Medicine, 15. Life on land, biology.organism_classification, Peanut, Agronomy, Cowpea, 16S-23S rRNA Internal Transcribed Spacer, Nitrogen fixation, Metabarcoding, Root Nodules, Plant, Biotechnology, Rhizobium
Abstract: Bradyrhizobia are Gram-negative soil bacteria that regroup a growing number of species. They are widespread in nature and recovered from various biomes that may be explained by a high genetic diversity in this genus. Among the numerous metabolic properties they can harbor, the nitrogen fixation resulting from the association with plants among which important crop legumes (soya bean, peanut, cowpea …) is of great interest, notably in a context of sustainable development. Metabarcoding is widely applied to study biodiversity from complex microbial communities. Here, we demonstrate that using a new species-specific and highly polymorphic 16S-23S rRNA intergenic spacer barcode, we could rapidly estimate the diversity of bradyrhizobial populations that associate with cowpea and peanut plants, two crop legumes of major interest in Senegal. Application of the method on indigenous bradyrhizobia associated with peanut and cowpea grown in soils collected in the center of the peanut basin shows that Bradyrhizobium vignae is a dominant symbiont. We also showed that the two plant species associate with distinct community profiles and that strains introduced by inoculation significantly modified the population structure with these two plants suggesting that application of elite strains as inoculants may well ensure optimized symbiotic performance. This approach may further be used to study the diversity of bradyrhizobia from contrasting agro-eco-climatic zones, to test whether the plant genotype influences the association outputs as well as to estimate the competitiveness for nodule occupancy and the fate of elite strains inoculated in the field. Key points • An amplicon sequencing approach targeting the Bradyrhizobium genus was developed. • Diversity of cowpea and peanut bradyrhizobia from cultivated soils was identified. • The method is well suited to test the competitiveness of defined Bradyrhizobium inoculants.
Published: 2021
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47. On the Threshold of Release of Confinement in an Epidemic SEIR Model Taking into Account the Protective Effect of Mask

Author: Pierre Auger, Ali Moussaoui, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Sorbonne Université (SU)-Universtié Yaoundé 1 [Cameroun]-Université Cadi Ayyad [Marrakech] (UCA)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Institut de Recherche pour le Développement (IRD [France-Nord]), Université Aboubekr Belkaid - University of Belkaïd Abou Bekr [Tlemcen], Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU), and Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord])
Subjects: 0301 basic medicine, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Urban Population, General Mathematics, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Immunology, Population, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], SEIR model, Models, Biological, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Disease susceptibility, 0302 clinical medicine, Econometrics, Humans, [MATH]Mathematics [math], education, Epidemics, Asymptomatic Infections, Pandemics, General Environmental Science, Mathematics, Urban mobility, Pharmacology, education.field_of_study, Travel, SARS-CoV-2, General Neuroscience, Masks, COVID-19, Mathematical Concepts, 3. Good health, Travel behavior, 030104 developmental biology, Computational Theory and Mathematics, 030220 oncology & carcinogenesis, Quarantine, Original Article, Mask protection, Disease Susceptibility, General Agricultural and Biological Sciences, Constant (mathematics), Covid-19, Confinement
Abstract: We present a classic SEIR model taking into account the daily movements of individuals in different places. The model also takes into account partial confinement of individuals. This model is coupled with a model of protection against the epidemic by the use of masks. We are studying the effects of combined confinement and protection measures on the dynamics of the epidemic. We consider a constant proportion of asymptomatic people. We assume that symptomatic infected people may change their urban travel behavior due to the disease which causes them to travel less to places where they used to move and to stay at home more often. We present a sensitivity study with respect to the parameters. We show that the combination of the use of masks with almost complete release of confinement makes it possible to avoid the occurrence of a secondary peak of the epidemic. The model predicts that a total release of confinement can be successful for an epidemic of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathcal {R}}_0 = 2.5$$\end{document}R0=2.5 if on average a proportion of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$60\%$$\end{document}60% of the population wears masks of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$60\%$$\end{document}60% efficacy. However, if \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$10\%$$\end{document}10% of the population remains confined, the same goal can be achieved with a proportion of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$80\%$$\end{document}80% of the population wearing masks with efficacy of the order of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$40\%$$\end{document}40%.
Published: 2021
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48. Soil microbial communities in the face of changing farming practices: A case study in an agricultural landscape in France

Author: Luc Biju-Duval, Solene Perrin, Christophe Lang, Mélanie Lelievre, Sébastien Terrat, Nicolas Chemidlin Prévost-Bouré, Laurie Dunn, Nicolas Marilleau, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord]), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU)
Subjects: Social Sciences, Forests, Agricultural soil science, Soil Microbiology, 2. Zero hunger, 0303 health sciences, Biomass (ecology), Multidisciplinary, Geography, Ecology, Microbiota, Agriculture, 04 agricultural and veterinary sciences, Biodiversity, Terrestrial Environments, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Medicine, France, Research Article, Agricultural methods, Soil ecology, Soil test, Science, Water stress, Soil Science, Crops, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Human Geography, complex mixtures, Ecosystems, 03 medical and health sciences, 030304 developmental biology, Land use, Bacteria, business.industry, Ecology and Environmental Sciences, Edaphology, Organisms, Biology and Life Sciences, 15. Life on land, Microbial population biology, 040103 agronomy & agriculture, Earth Sciences, 0401 agriculture, forestry, and fisheries, Species richness, business, Crop Science
Abstract: International audience; According to biogeography studies, the abundance and richness of soil microorganisms vary across multiple spatial scales according to soil properties and farming practices. However, soil microorganisms also exhibit poorly understood temporal variations. This study aimed at better understanding how soil microbial communities respond to changes in farming practices at a landscape scale over time. A regular grid of 269 sites was set up across a 1,200 ha farming landscape, and soil samples were characterized for their molecular microbial biomass and bacterial richness at two dates (2011 and 2016). A mapping approach highlighted that spatial microbial patterns were stable over time, while abundance and richness levels were modified. The drivers of these changes were investigated though a PLS-PM (partial least square path-modeling) approach. Soil properties were stable over time, but farming practices changed. Molecular microbial biomass was mainly driven by soil resources, whereas bacterial richness depended on both farming practices and ecological parameters. Previous-crop and management effects and a temporal dependence of the microbial community on the historical farming management were also highlighted.
Published: 2021
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49. Sibling status, home birth, tattoos and stitches are risk factors for chronic hepatitis B virus infection in Senegalese children: A cross‐sectional survey

Author: Périères, Lauren, Protopopescu, Camelia, Lo, Gora, Marcellin, Fabienne, Ba, El Hadji, Coste, Marion, Touré Kane, Coumba, Diallo, Aldiouma, Sokhna, Cheikh, Boyer, Sylvie, Anrs 12356 Ambass Survey Study, Grp, Bérenger, Cyril, Bousmah, Marwân-Al-Qays, Carrieri, Patrizia, de Sèze, Maëlle, Djaogol, Tchadine, Maradan, Gwenaëlle, Treibich, Carole, Ba Ba, El Hadji, Dièye, Fambaye, Diouf, Assane, Faye, Elhadji Bilal, Ndiaye, Assane, Sow, Mouhamadou Baba, Ndiaye, Anna Julienne Selbé, Ndiour, Samba, Halfon, Philippe, Mohamed, Sofiane, Rouveau, Nicolas, Cortès, Maria‐camila Calvo, Laborde‐balen, Gabrièle, Audibert, Martine, Fall, Fatou, Gueye, Ibrahima, Lacombe, Karine, Seydi, Moussa, Shimakawa, Yusuke, Tuaillon, Edouard, Vray, Muriel, Maladies infectieuses persistantes et émergentes en Afrique de l’Ouest [Dakar, Sénégal] (Equipe 3 - VITROME), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation [Dakar, Sénégal] (IRESSEF), Aix-Marseille Sciences Economiques (AMSE), École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), The AmBASS research project was funded in full by the French ANRS Emerging Infectious Diseases research agency under the auspices of the French National Institute for Health and Medical Research (INSERM) (INSERM-ANRS), grant number 12356., Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Pathogenesis and Control of Chronic and Emerging Infections (PCCEI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université des Antilles (UA)-Etablissement français du don du sang [Montpellier], Lhuillier, Elisabeth, and École des hautes études en sciences sociales (EHESS)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)
Subjects: HBsAg, Cross-sectional study, medicine.disease_cause, 0302 clinical medicine, Pregnancy, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Infection control, risk factors, 030212 general & internal medicine, [SHS.ECO] Humanities and Social Sciences/Economics and Finance, Home Childbirth, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, child, Tattooing, virus diseases, Hepatitis B, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Senegal, 3. Good health, Vaccination, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, 030211 gastroenterology & hepatology, Hepatitis B virus, prevalence, 03 medical and health sciences, Hepatitis B, Chronic, Virology, medicine, Humans, Hepatitis B Vaccines, Sibling, Aged, Hepatitis B Surface Antigens, Hepatology, business.industry, Siblings, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, medicine.disease, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Infectious Disease Transmission, Vertical, digestive system diseases, Cross-Sectional Studies, hepatitis B, business, Home birth, Demography
Abstract: International audience; Sub-Saharan Africa's hepatitis B virus (HBV) burden is primarily due to infection in infancy. However, data on chronic HBV infection prevalence and associated risk factors in children born post-HBV vaccination introduction are scarce. We estimated hepatitis B surface antigen (HBsAg) prevalence and risk factors in Senegalese children born during the HBV vaccination era. In 2018-2019, a community-based cross-sectional survey was conducted in Senegal among children born between 2004 and 2015 (ie after the three-dose HBV vaccine series was introduced (2004) but before the birth dose's introduction (2016)). HBsAg-positive children were identified using dried blood spots. A standardized questionnaire collected socioeconomic information. Data were age-sex weighted and calibrated to be representative of children living in the study area. Risk factors associated with HBsAg positivity were identified using negative binomial regression. Among 1,327 children, 17 were HBsAg-positive (prevalence = 1.23% (95% confidence interval [CI] 0.61-1.85)). Older age (adjusted incidence-rate ratio [aIRR] 1.31 per one-year increase, 95% CI 1.10-1.57), home vs healthcare facility delivery (aIRR 3.55, 95% CI 1.39-9.02), stitches (lifetime) (aIRR 4.79; 95% CI 1.84-12.39), tattoos (aIRR 8.97, 95% CI 1.01-79.11) and having an HBsAg-positive sibling with the same mother (aIRR 3.05, 95% CI 1.09-8.57) were all independently associated with HBsAg positivity. The low HBsAg prevalence highlights the success of the Senegalese HBV vaccination program. To further reduce HBV acquisition in children, high-risk groups, including pregnant women and siblings of HBsAg-positive individuals, must be screened. Vital HBV infection prevention measures include promoting delivery in healthcare facilities, and increasing awareness of prevention and control procedures.
Published: 2021
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50. Individual and healthcare supply-related barriers to treatment initiation in HIV-positive patients enrolled in the Cameroonian antiretroviral treatment access programme

Author: M Ngo Tonye, R B Pallawo, Issiakou Adamou, I Wandji, P Momo, B Spire, E Mpoudi-Ngolé, N Manga, E Njom Nlend, J M Bob Oyono, E Kamto, G Touko, B Fangam Molu, D Eloundou, H Mossi, M Tsoungi Akoa, U Olinga, H Meli, G Maradan, Pierre-Julien Coulaud, Laurent Vidal, M Ndam, R Garcia, J D Ngan Bilong, A Guterrez, Boyer, Christopher Kuaban, E Delaporte, C Tong, A P Meledie Ndjong, Y Perfura, C Nouboue, A Mafuta, G Tchatchoua, J Dissongo, N Noumssi, S Omgnesseck, J J Ze, Christian Laurent, Bruno Spire, O Ossanga, F Chabrol, C Ewolo, A Ambani, S Boyer, E Belley Priso, M C Kuitcheu, M Fokoua, E Kouakam, L J G Buffeteau, H Essama Owona, Khadim Ndiaye, S Eymard-Duvernay, Sylvie Boyer, F Liégeois, C Tchimou, M Mora, J D Noah, S Beke, E Abeng Mbozo’o, L R Njock, L March, M J Gomez, J Djene, C Danwe, Camelia Protopopescu, S Ngwane, H Fokam, E Soh, C Ndjie Essaga, O Kouambo, C Laurent, G Temgoua, M T Mengue, Gwenaëlle Maradan, Maël Baudoin, A Simo Ndongo, D S.Maninzou, L Ndalle, B Taman, Ida Penda, M Mpoudi Ngole, C Biloa, Ngam Engonwei, E H Moby, J Meli, L J Bitang, M Mbangue, L Ayangma, P Thumerel, O Ndalle, B Mbatchou, M Suzan-Monti, M Mgantcha, A L Mawe, S Abia, J Hachu, H Nyemb, P J Fouda, L Sagaon-Teyssier, H Hadja, L Ngum, F Ndoumbe, Y Mapoure, H Abessolo, I Ngo, A Yeffou, C Bondze, J Lindou, A Malongue, C Kouanfack, M de Sèze, P Ateba, Z Nanga, B Takou, M Defo, E C Njitoyap Ndam, C Ejangue, A Nono Toche, I Seyep, Yoyo Ngongang, Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Université de Yaoundé I, EVOLCam Group: G Maradan, A Ambani, O Ndalle, P Momo, C Tong, S Boyer, V Boyer, L March, M Mora, L Sagaon-Teyssier, M de Sèze, B Spire, M Suzan-Monti, C Laurent, F Liégeois, E Delaporte, V Boyer, S Eymard-Duvernay, F Chabrol, E Kouakam, O Ossanga, H Essama Owona, C Biloa, M-T Mengue, E Mpoudi-Ngolé, P J Fouda, C Kouanfack, H Abessolo, N Noumssi, M Defo, H Meli, Z Nanga, Y Perfura, M Ngo Tonye, O Kouambo, U Olinga, E Soh, C Ejangue, E Njom Nlend, A Simo Ndongo, E Abeng Mbozo'o, M Mpoudi Ngole, N Manga, C Danwe, L Ayangma, B Taman, E C Njitoyap Ndam, B Fangam Molu, J Meli, H Hadja, J Lindou, J M Bob Oyono, S Beke, D Eloundou, G Touko, J J Ze, M Fokoua, L Ngum, C Ewolo, C Bondze, J D Ngan Bilong, D S Maninzou, A Nono Toche, M Tsoungi Akoa, P Ateba, S Abia, A Guterrez, R Garcia, P Thumerel, E Belley Priso, Y Mapoure, A Malongue, A P Meledie Ndjong, B Mbatchou, J Hachu, S Ngwane, J Dissongo, M Mbangue, Ida Penda, H Mossi, G Tchatchoua, Yoyo Ngongang, C Nouboue, I Wandji, L Ndalle, J Djene, M J Gomez, A Mafuta, M Mgantcha, E H Moby, M C Kuitcheu, A L Mawe, Ngam Engonwei, L J Bitang, M Ndam, R B Pallawo, Issiakou Adamou, G Temgoua, C Ndjie Essaga, C Tchimou, A Yeffou, I Ngo, H Fokam, H Nyemb, L R Njock, S Omgnesseck, E Kamto, B Takou, L J-G Buffeteau, F Ndoumbe, J-D Noah, I Seyep, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), and Herrada, Anthony
Subjects: Adult, medicine.medical_specialty, Anti-HIV Agents, 030231 tropical medicine, HIV Infections, Disease, Disease cluster, 03 medical and health sciences, 0302 clinical medicine, healthcare supply-related factors, Interquartile range, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Health care, medicine, Humans, 030212 general & internal medicine, Cameroon, Proportional hazards model, business.industry, Health Policy, Hazard ratio, HIV, Hepatitis B, medicine.disease, 3. Good health, time to ART initiation, Cross-Sectional Studies, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Family medicine, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Population study, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Delivery of Health Care, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Increasing demand for antiretroviral treatment (ART) together with a reduction in international funding during the last decade may jeopardize access to ART. Using data from a cross-sectional survey conducted in 2014 in 19 HIV services in the Centre and Littoral regions in Cameroon, we investigated the role of healthcare supply-related factors in time to ART initiation in HIV-positive patients eligible for ART at HIV diagnosis. HIV service profiles were built using cluster analysis. Factors associated with time to ART initiation were identified using a multilevel Cox model. The study population included 847 HIV-positive patients (women 72%, median age: 39 years). Median (interquartile range) time to ART initiation was 1.6 (0.5–4.3) months. Four HIV service profiles were identified: (1) small services with a limited staff practising partial task-shifting (n = 4); (2) experienced and well-equipped services practising task-shifting and involving HIV community-based organizations (n = 5); (3) small services with limited resources and activities (n = 6); (4) small services providing a large range of activities using task-shifting and involving HIV community-based organizations (n = 4). The multivariable model showed that HIV-positive patients over 39 years old [hazard ratio: 1.26 (95% confidence interval) (1.09–1.45), P = 0.002], those with disease symptoms [1.21 (1.04–1.41), P = 0.015] and those with hepatitis B co-infection [2.31 (1.15–4.66), P = 0.019] were all more likely to initiate ART early. However, patients in the first profile were less likely to initiate ART early [0.80 (0.65–0.99), P = 0.049] than those in the second profile, as were patients in the third profile [association only significant at the 10% level; 0.86 (0.72–1.02), P = 0.090]. Our findings provide a better understanding of the role played by healthcare supply-related factors in ART initiation. In HIV services with limited capacity, task-shifting and support from community-based organizations may improve treatment access. Additional funding is required to relieve healthcare supply-related barriers and achieve the goal of universal ART access.
Published: 2021
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