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1. The influence of habitat on viral diversity in neotropical rodent hosts

Author

Anne Lavergne, Damien Donato, Alain Franc, Sourakhata Tirera, Benoit de Thoisy, Christiane Bouchier, Vincent Lacoste, Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut Pasteur [Paris], Département de Virologie - Department of Virology, Arbovirus & Emerging Viral Diseases [Vientiane] (A&EVD), Institut Pasteur du Laos, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), S. Tirera was funded by the RESERVOIRS program, supported by European funds (PO FSE 2014-2020), an 'Investissement d’Avenir' grant managed by the Agence Nationale de la Recherche (CEBA, ref. ANR-10-LABX-25-01), a European Commission 'REGPOT-CT-2011-285837-STRonGer' grant within the FP7, and the Institut Pasteur de la Guyane. This study was conducted within the 'BioViRo' program, supported by an 'Investissement d’Avenir' grant managed by the Agence Nationale de la Recherche (CEBA, reference ANR-10-LABX-25-01). Field work conducted by BdT was funded by the ViRUSES program, supported by European funds (FEDER) and assistance from Région Guyane and Direction Régionale pour la Recherche et la Technologie, the ZNIEFF Guyane (DEAL Guyane) program, the GUYAMAZON II program, and Réseau des Observatoires Hommes-Milieux (OHM-Oyapok APR 2013, François Catzeflis). High-throughput sequencing was performed on the Biomics Platform, C2RT, Institut Pasteur, Paris, France, supported by France Génomique (ANR-10-INBS-09-09) and IBISA., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 285837,EC:FP7:REGPOT,FP7-REGPOT-2011-1,STRONGER(2011), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), and Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest

Subjects
Viral ecology, Ecology (disciplines), viruses, Rodentia, Forests, Biology, Microbiology, Rodents, Article, Viral phylogenies, 03 medical and health sciences, Amazonia, Abundance (ecology), Zoonoses, Virology, Animals, Human virome, Alpha diversity, Ecosystem, Phylogeny, 030304 developmental biology, 0303 health sciences, Ecology, 030306 microbiology, Host (biology), Virome, Genetic Variation, 15. Life on land, QR1-502, 3. Good health, Infectious Diseases, Habitat, Metagenomics, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDE]Environmental Sciences, Metagenome, Species richness
Abstract

Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host’s dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems.

Published
2021
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2. Paramyxovirus circulation in bat species from French Guiana

Author

Vincent Lacoste, Damien Donato, Anne Lavergne, Edith Darcissac, Benoit de Thoisy, Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Réseau International des Instituts Pasteur (RIIP), Département de Virologie - Department of Virology, Institut Pasteur [Paris] (IP), This study was funded by the CAROLIA and RESERVOIRS programs supported by European Funds (ERDF/FEDER), the Région Guyane and the Direction Régionale pour la Recherche et la Technologie. It also received 'Investissement d'Avenir' grants managed by the Agence Nationale de la Recherche (CEBA, Ref. ANR-10-LABX-25-01)., and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)

Subjects
0301 basic medicine, Microbiology (medical), animal structures, Highly pathogenic, viruses, 030106 microbiology, Zoology, Cross-species transmission, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Mormoopidae, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Genus, Chiroptera, Pteronotus, Bats, Genetics, Animals, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Carollia perspicillata, Paramyxoviridae Infections, biology, Phylogenetic tree, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], biochemical phenomena, metabolism, and nutrition, biology.organism_classification, French Guiana, 030104 developmental biology, Infectious Diseases, Paramyxoviridae, Paramyxoviruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Desmodus rotundus, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Phylogenetic relationships, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Bats are recognized as reservoirs of numerous viruses. Among them, paramyxoviruses, for example, Hendra and Nipah viruses, are highly pathogenic to humans. Nothing is known regarding the circulation of this viral family in bats from French Guiana. To search for the presence of paramyxoviruses in this territory, 103 bats of seven different species were sampled and screened using a molecular approach. Four distinct paramyxovirus sequences were detected from three bat species (Desmodus rotundus, Carollia perspicillata, and Pteronotus alitonus) at high prevalence rates. In D. rotundus, two types of paramyxovirus cocirculate, with most of the bats co-infected. The phylogenetic analysis of these sequences revealed that three of them were closely related to previously characterized sequences from D. rotundus, C. perspicillata, and P. parnellii from Brazil and Costa Rica. The fourth sequence, identified in D. rotundus, was closely related to the one detected in P. alitonus in French Guiana and to previously described sequences detected in P. parnellii in Costa Rica. All paramyxovirus sequences detected in this study are close to the Jeilongvirus genus. Altogether, our results and those of previous studies indicate a wide geographical distribution of these paramyxoviruses (from Central to South America) and suggest potential cross-species transmissions of paramyxoviruses between two different bat families: Mormoopidae (P. alitonus) and Phyllostomidae (D. rotundus). In addition, their closeness to paramyxoviruses identified in rodents emphasizes the need to investigate the role of these animals as potential reservoirs or incidental hosts. Finally, the high prevalence rates of some paramyxoviruses in certain bat species, associated with the presence of large bat colonies and, in some cases, their potential proximity with humans are all parameters that can contribute to the risk of cross-species transmission between bat species and to the emergence of new paramyxoviruses in humans, a risk that deserves further investigation.

Published
2021
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3. Maripa Virus RNA Load and Antibody Response in Hantavirus Pulmonary Syndrome, French Guiana

Author

Anne Lavergne, Hatem Kallel, Séverine Matheus, Claire Mayence, Dominique Rousset, Vincent Lacoste, Stéphanie Houcke, Benoit de Thoisy, Bhety Labeau, David Moua, Alexandre Roux, Damien Donato, Didier Hommel, Laetitia Bremand, Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), This study was supported in part by the Centre National de Référence des Hantavirus Laboratoire Associé financed by the Institut Pasteur de la Guyane and Santé Publique France (Saint-Maurice, France). This study benefited from the RESERVOIRS program, which is supported by the European Regional Development Fund and Fonds Européen de Developpement Régional, and received assistance from Région Guyane and Direction Régionale pour la Recherche et la Technologie and Investissement d’Avenir grants managed by the Agence Nationale de la Recherche (CEBA ANR-10-LABEX-25-01)., We thank Sandrine Fernandes-Pellerin and Nathalie Jolly for their helpful expertise on ethics issues relevant to this study. In addition, we acknowledge Thierry Carage for his assistance., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), and ANR-10-LABX-25-01/10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)

Subjects
Male, 0301 basic medicine, Orthohantavirus, Epidemiology, viruses, lcsh:Medicine, hantavirus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Hantavirus Pulmonary Syndrome/mortality, Medicine, MESH: Hantavirus / immunology, MESH: Aged, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Middle Aged, biology, MESH: RNA, Viral/blood, Dispatch, MESH: Hantavirus/immunology, MESH: Hantavirus Pulmonary Syndrome/diagnosis, Middle Aged, Viral Load, MESH: Hantavirus Pulmonary Syndrome / virology, French Guiana, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, arboviruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Viral, Maripa virus, MESH: RNA, Viral / blood, Antibody, MESH: Viral Load, Viral load, Maripa Virus RNA Load and Antibody Response in Hantavirus Pulmonary Syndrome, French Guiana, Adult, Microbiology (medical), MESH: Hantavirus Pulmonary Syndrome / diagnosis, hantavirus pulmonary syndrome, MESH: Hantavirus/isolation & purification, Virus, lcsh:Infectious and parasitic diseases, Diagnosis, Differential, 03 medical and health sciences, Immune system, MESH: Diagnosis, Differential, MESH: Hantavirus Pulmonary Syndrome / mortality, MESH: French Guiana, MESH: Hantavirus / isolation & purification, Humans, lcsh:RC109-216, MESH: Hantavirus Pulmonary Syndrome/virology, Aged, Hantavirus, Hantavirus pulmonary syndrome, MESH: Humans, business.industry, lcsh:R, RNA, MESH: Adult, antibody response, Virology, MESH: Male, 030104 developmental biology, Antibody response, biology.protein, business
Abstract

International audience; We report viral RNA loads and antibody responses in 6 severe human cases of Maripa virus infection (2 favorable outcomes) and monitored both measures during the 6-week course of disease in 1 nonfatal case. Further research is needed to determine prevalence of this virus and its effect on other hantaviruses.

Published
2018
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4. Novel herpesviruses in neotropical bats and their relationship with other members of the Herpesviridae family

Author

Damien Donato, Anne Lavergne, Benoit de Thoisy, Vincent Lacoste, Samantha James, Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Ecole Doctorale 587 : Diversités, santé et développement en Amazonie (ED 587), Université de Guyane (UG), Département de Virologie - Department of Virology, Institut Pasteur [Paris] (IP), Biologie des Infections Virales Émergentes - Biology of Emerging Viral Infections (UBIVE), 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)-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)-Institut Pasteur [Paris] (IP), This study benefited from the CAROLIA and RESERVOIRS programs supported by European funds (ERDF/FEDER) and assistance from Région Guyane and Direction Régionale pour la Recherche et la Technologie. It also received a European Commission 'REGPOT-CT-2011-285837-STRonGer' grant within the FP7 and 'Investissement d'Avenir' grants managed by the Agence Nationale de la Recherche (CEBA, Ref. ANR-10-LABX-25-01). S.J. was supported by a grant from the Université de la Guyane, Ecole doctorale 587 'Diversités, Santé et Développement en Amazonie' and by a grant from the Collectivité Territoriale de la Guyane., All field volunteers and owners and/or managers of capture sites are warmly acknowledged for their assistance in captures., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), European Project: 285837,EC:FP7:REGPOT,FP7-REGPOT-2011-1,STRONGER(2011), Lacoste, Vincent, Laboratoires d'excellence - CEnter of the study of Biodiversity in Amazonia - - CEBA2010 - ANR-10-LABX-0025 - LABX - VALID, Strengthening transdisciplinary research on infectious and emerging diseases in French Guiana: linking fieldwork, benchside and bedside - STRONGER - - EC:FP7:REGPOT2011-11-01 - 2015-04-30 - 285837 - VALID, Centre International de Recherche en Infectiologie - UMR (CIRI), 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)-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)-Institut Pasteur [Paris] (IP), Institut Pasteur [Paris], and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], DNA-Directed DNA Polymerase, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Mormoopidae, law.invention, law, Chiroptera, Gammaherpesvirinae, Molossidae, Herpesviridae, Phylogeny, Polymerase chain reaction, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Carollia perspicillata, biology, Phylogenetic tree, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Betaherpesvirus, French Guiana, 3. Good health, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Glycoprotein B, Microbiology (medical), Evolution, 030106 microbiology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, DNA polymerase, Microbiology, Article, Gammaherpesvirus, Viral Proteins, 03 medical and health sciences, Phylogenetics, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetics, Animals, Martinique, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Glycoproteins, biology.organism_classification, Exodeoxyribonucleases, 030104 developmental biology, Evolutionary biology, Desmodus rotundus, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract

In the past decade, a large number of studies have detected herpesvirus sequences from many bat species around the world. Nevertheless, the discovery of bat herpesviruses is geographically uneven. Of the various bat species tested to date, only a few were from the New World. Seeking to investigate the distribution and diversity of herpesviruses circulating in neotropical bats, we carried out molecular screening of 195 blood DNA samples from 11 species of three bat families (Phyllostomidae, Mormoopidae, and Molossidae). Using polymerase chain reaction amplification, with degenerate consensus primers targeting highly conserved amino acid motifs of the herpesvirus DNA polymerase and Glycoprotein B genes, we characterized novel viral sequences from all tested species. BLAST searches, pairwise nucleotide and amino acid sequence comparisons, as well as phylogenetic analyses confirmed that they all belonged to the Herpesviridae family, of the Beta- and Gammaherpesvirinae subfamilies. Fourteen partial DNA polymerase gene sequences, of which three beta- and 11 gamma-herpesviruses, were detected. A total of 12 partial Glycoprotein B gene sequences, all gamma-herpesviruses, were characterized. Every sequence was specific to a bat species and in some species (Desmodus rotundus, Carollia perspicillata, and Pteronotus rubiginosus) multiple viruses were found. Phylogenetic analyses of beta- and gammaherpesvirus sequences led to the identification of bat-specific clades. Those composed of sequences obtained from different bat species belonging to distinct subfamilies follow the taxonomy of bats. This study confirms the astonishing diversity of bat herpesviruses and broadens our knowledge of their host range. Nevertheless, it also emphasizes the fact that, to better appreciate the evolutionary history of these viruses, much remains to be done at various taxonomic levels., Highlights • Molecular screening was carried out on 11 bat species from French Guiana and Martinique (French West Indies). • Partial DNA polymerase gene sequences of 14 viruses were characterized, three beta- and 11 gammaherpesviruses, as well as 12 Glycoprotein B sequences, all of gamma-herpesviruses. • Genetic characterization of these sequences reveals a high degree of genetic divergence. • On a phylogenetic viewpoint, most of the newly discovered herpesvirus sequences fall within bat-specific clades well correlated with the taxonomy of their hosts. • This study is the largest conducted to date in terms of species diversity from the New World.

Published
2020
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5. Unraveling the genetic diversity and phylogeny of Leishmania RNA virus 1 strains of infected Leishmania isolates circulating in French Guiana

Author

Emilie Mosnier, Marine Ginouves, Vincent Vantilcke, Vincent Lacoste, Eliane Bourreau, Ignacio S. Caballero, Christiane Bouchier, Damien Donato, Sourakhata Tirera, Pierre Couppié, Anne Lavergne, Ghislaine Prévot, Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Ecosystemes Amazoniens et Pathologie Tropicale (EPat), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Guyane (UG), Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Boston University [Boston] (BU), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), Centre Hospitalier de l'Ouest Guyanais, Département de Virologie - Department of Virology, ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 285837,EC:FP7:REGPOT,FP7-REGPOT-2011-1,STRONGER(2011), Lacoste, Vincent, Laboratoires d'excellence - CEnter of the study of Biodiversity in Amazonia - - CEBA2010 - ANR-10-LABX-0025 - LABX - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Strengthening transdisciplinary research on infectious and emerging diseases in French Guiana: linking fieldwork, benchside and bedside - STRONGER - - EC:FP7:REGPOT2011-11-01 - 2015-04-30 - 285837 - VALID, and Institut Pasteur [Paris]

Subjects
0301 basic medicine, Male, MESH: Leishmaniavirus, MESH: Sequence Analysis, DNA, MESH: Leishmaniasis, [SDV]Life Sciences [q-bio], 0302 clinical medicine, Medicine and Health Sciences, Cluster Analysis, MESH: Genetic Variation, MESH: Phylogeny, Leishmaniasis, Phylogeny, Data Management, Genetics, Protozoans, Leishmania, MESH: Aged, MESH: Middle Aged, Phylogenetic tree, lcsh:Public aspects of medicine, Database and informatics methods, Sequence analysis, Phylogenetic Analysis, Middle Aged, 3. Good health, French Guiana, Phylogenetics, [SDV] Life Sciences [q-bio], Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Young Adult, MESH: RNA, Viral, RNA, Viral, Female, MESH: Genome, Viral, Research Article, Adult, Computer and Information Sciences, lcsh:Arctic medicine. Tropical medicine, lcsh:RC955-962, Bioinformatics, MESH: Leishmania, 030231 tropical medicine, Leishmaniavirus, MESH: Sequence Alignment, Nucleotide Sequencing, Genome, Viral, Biology, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, 03 medical and health sciences, Young Adult, Cutaneous leishmaniasis, Sequence Motif Analysis, MESH: French Guiana, medicine, Parasitic Diseases, Humans, Evolutionary Systematics, Molecular Biology Techniques, Sequencing Techniques, Genotyping, Molecular Biology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, DNA sequence analysis, Taxonomy, Aged, Evolutionary Biology, MESH: Humans, Public Health, Environmental and Occupational Health, Organisms, Biology and Life Sciences, Genetic Variation, RNA virus, lcsh:RA1-1270, MESH: Adult, Sequence Analysis, DNA, medicine.disease, biology.organism_classification, MESH: Cluster Analysis, Parasitic Protozoans, MESH: Male, Research and analysis methods, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Sequence Alignment, MESH: Female
Abstract

Introduction Leishmania RNA virus type 1 (LRV1) is an endosymbiont of some Leishmania (Vianna) species in South America. Presence of LRV1 in parasites exacerbates disease severity in animal models and humans, related to a disproportioned innate immune response, and is correlated with drug treatment failures in humans. Although the virus was identified decades ago, its genomic diversity has been overlooked until now. Methodology/Principles findings We subjected LRV1 strains from 19 L. (V.) guyanensis and one L. (V.) braziliensis isolates obtained from cutaneous leishmaniasis samples identified throughout French Guiana with next-generation sequencing and de novo sequence assembly. We generated and analyzed 24 unique LRV1 sequences over their full-length coding regions. Multiple alignment of these new sequences revealed variability (0.5%–23.5%) across the entire sequence except for highly conserved motifs within the 5’ untranslated region. Phylogenetic analyses showed that viral genomes of L. (V.) guyanensis grouped into five distinct clusters. They further showed a species-dependent clustering between viral genomes of L. (V.) guyanensis and L. (V.) braziliensis, confirming a long-term co-evolutionary history. Noteworthy, we identified cases of multiple LRV1 infections in three of the 20 Leishmania isolates. Conclusions/Significance Here, we present the first-ever estimate of LRV1 genomic diversity that exists in Leishmania (V.) guyanensis parasites. Genetic characterization and phylogenetic analyses of these viruses has shed light on their evolutionary relationships. To our knowledge, this study is also the first to report cases of multiple LRV1 infections in some parasites. Finally, this work has made it possible to develop molecular tools for adequate identification and genotyping of LRV1 strains for diagnostic purposes. Given the suspected worsening role of LRV1 infection in the pathogenesis of human leishmaniasis, these data have a major impact from a clinical viewpoint and for the management of Leishmania-infected patients., Author summary Leishmaniasis is a well-known parasitosis due to an infection by the protozoan Leishmania parasites firmly established in South America. In French Guiana, where leishmaniasis is a public health problem, having an annual incidence of 5.6 cases/10,000 inhabitants, 80% of Leishmania spp. parasites are infected by an endosymbiotic virus, Leishmania RNA virus 1 (LRV1). The purpose of this study was to gain insights on the genetic variability and evolution of LRV1 at the genomic level. We subjected 20 Leishmania isolates obtained from cutaneous lesions with next generation sequencing and de novo sequence assembly. This allowed generating 24 LRV1 full-length coding sequences presenting among themselves a significant genetic diversity. The inferred phylogenetic relationships enabled to identify distinct well-supported genotypes and support the hypothesis of co-evolution between LRV1 strains and their parasite hosts. In addition, we identified multiple LRV1 infections in three parasite isolates. Based on these data, future characterization of new strains from other geographic areas and other parasite species should extend knowledge of LRV1 diversification processes. Finally, these results allowed us to identify genomic regions where best to allocate resources for subsequent analyses of LRV1 viral diversity and genotyping that could serve for accurate routine molecular diagnostic applications.

Published
2017
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6. HIV-1 Pol Gene Polymorphism and Antiretroviral Resistance Mutations in Treatment-Naive Adult Patients in French Guiana Between 2006 and 2012

Author

Anne Lavergne, Leila Adriouch, Félix Djossou, Myriam El Guedj, Mathieu Nacher, Vincent Lacoste, Alain Berlioz-Arthaud, Edith Darcissac, Pierre Couppié, Rachida Boukhari, Edouard Tanguy, Emmanuelle Papot, Vincent Vantilcke, Damien Donato, Jean-François Pouliquen, Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), 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], Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Centre Hospitalier de l'Ouest Guyanais Franck Joly (Saint-Laurent-du-Maroni), Unité des Maladies Infectieuses et Tropicales [Cayenne, Guyanne Française], This work was funded by the Institut Pasteur de la Guyane. It has also benefited from a European commission REGPOT-CT-2011-285837-STRonGer grant within the FP7, The authors thank Nathalie Jolly from the Institut Pasteur Clinical Research Department (PIRC, Pôle Intégré de Recherche Clinique) for her help in the ethical aspects of the project. They also thank Ketty Bienvenu, Lidia Saint Louis, Sergine Soyon, and Karine Verin for their invaluable assistance., European Project: 285837,EC:FP7:REGPOT,FP7-REGPOT-2011-1,STRONGER(2011), Lacoste, Vincent, Strengthening transdisciplinary research on infectious and emerging diseases in French Guiana: linking fieldwork, benchside and bedside - STRONGER - - EC:FP7:REGPOT2011-11-01 - 2015-04-30 - 285837 - VALID, and 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)

Subjects
0301 basic medicine, Male, [SDV]Life Sciences [q-bio], HIV Infections, Drug resistance, MESH: Genotype, 0302 clinical medicine, MESH: HIV Protease/genetics, HIV Protease, MESH: HIV-1/growth & development, Polymorphism (computer science), Genotype, 030212 general & internal medicine, Genetics, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Aged, MESH: HIV Infections/epidemiology, Molecular Epidemiology, MESH: Middle Aged, Incidence (epidemiology), MESH: HIV Infections/drug therapy, Middle Aged, Viral Load, MESH: HIV Infections/virology, MESH: HIV-1/genetics, HIV Reverse Transcriptase, 3. Good health, French Guiana, [SDV] Life Sciences [q-bio], MESH: HIV Protease Inhibitors/therapeutic use, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Reverse Transcriptase Inhibitors, Female, Viral load, Adult, MESH: French Guiana/epidemiology, Immunology, Biology, MESH: Reverse Transcriptase Inhibitors/therapeutic use, MESH: Drug Resistance, Viral/genetics, 03 medical and health sciences, MESH: Polymorphism, Genetic, MESH: Viral Load/drug effects, Acquired immunodeficiency syndrome (AIDS), Virology, Drug Resistance, Viral, medicine, Humans, MESH: Molecular Epidemiology, MESH: HIV Reverse Transcriptase/genetics, Aged, Retrospective Studies, Genetic diversity, Polymorphism, Genetic, MESH: Humans, Molecular epidemiology, MESH: Adult, MESH: Retrospective Studies, HIV Protease Inhibitors, medicine.disease, MESH: Male, 030104 developmental biology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Mutation, HIV-1, MESH: Mutation, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Female, MESH: HIV-1/drug effects
Abstract

International audience; Little information is available on the molecular epidemiologic profile of HIV-1 in French Guiana, the French department with the highest HIV/AIDS incidence. To follow the evolution of HIV-1 diversity, we carried out a molecular analysis of HIV-1 isolates from 305 treatment-naive patients between 2006 and 2012. Protease and reverse-transcriptase sequences were obtained for subtype characterization, polymorphism analysis, and identification of drug resistance mutations. Of 305 HIV-1 strains, 95.1% were subtype B viruses. The overall prevalence of transmitted drug-resistance mutations (TDRMs) was 4.6% (14/305), ranging from 1.9% to 7.1% depending on the year. This study shows a low level of HIV-1 genetic diversity and a moderate prevalence of TDRMs with no evidence of an increasing trend over the study period. Nevertheless, the strong genetic polymorphism observed on both genes may be of concern for long-term treatment of people living with HIV-1 and thus deserves continuous monitoring.

Published
2016
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7. Bioecological Drivers of Rabies Virus Circulation in a Neotropical Bat Community

Author

Benoit de Thoisy, Anne Lavergne, Dominique Pontier, Rachel Lavenir, Damien Donato, Hervé Bourhy, Laurent Dacheux, Arielle Salmier, Vincent Lacoste, Marguerite Delaval, Edith Darcissac, Amandine Guidez, Florence Larrous, Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre National de Référence de la Rage-Dynamique des Lyssavirus et adaptation à l'hôte (CNR), Institut Pasteur [Paris] (IP), Service développement Sylvétude [Réserve Montabo, Cayenne], ONF - Direction régionale de la Guyane [Cayenne], Office national des forêts (ONF)-Office national des forêts (ONF), Ecoépidémiologie évolutionniste, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), This study was conducted within the ViRUSES and CAROLIA programs supported by European funds (ERDF/FEDER) and assistance from Région Guyane and Direction Régionale pour la Recherche et la Technologie. It also received a European commission REGPOT-CT-2011-285837-STRonGer' grant within the FP7 and 'Investissement d’ Avenir' Grants managed by Agence Nationale de la Recherche (CEBA, Ref. ANR-10- LABX-25-01 ECOFECT, Ref. ANR-11-LABX-0048). The authors thank the Institut de Veille Sanitaire, Saint-Maurice, France (http://www.invs.sante.fr/) and the Institut Pasteur for their financial contribution to the NationalReference Centre for Rabies that made this work possible. This research was also funded by the European Union Seventh framework Programme (FP7/2007-2013) PREDEMICS grant 278433., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-11-LABX-0048,ECOFECT,Dynamiques eco-évolutives des maladies infectieuses(2011), European Project: ERDF/FEDER,ViRUSES, European Project: 285837,EC:FP7:REGPOT,FP7-REGPOT-2011-1,STRONGER(2011), European Project: 278433,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PREDEMICS(2011), Institut Pasteur [Paris], and Office National des Forêts (ONF)-Office National des Forêts (ONF)

Subjects
Male, RNA viruses, 0301 basic medicine, Viral Diseases, viruses, [SDV]Life Sciences [q-bio], Forests, Animal Phylogenetics, Antibodies, Viral, Pathology and Laboratory Medicine, medicine.disease_cause, Chiroptera, Zoonoses, Bats, Medicine and Health Sciences, Phylogeny, Data Management, Mammals, Ecology, Transmission (medicine), lcsh:Public aspects of medicine, Terrestrial Environments, French Guiana, Habitats, Phylogenetics, Serology, Infectious Diseases, Community Ecology, Medical Microbiology, Viral Pathogens, Vertebrates, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Neglected tropical diseases, Female, Pathogens, Brazil, Research Article, Neglected Tropical Diseases, Computer and Information Sciences, lcsh:Arctic medicine. Tropical medicine, Rabies, lcsh:RC955-962, Biology, Microbiology, Ecosystems, Rabies Virus, 03 medical and health sciences, medicine, Animals, Evolutionary Systematics, Microbial Pathogens, Ecosystem, Taxonomy, Evolutionary Biology, Ecology and Environmental Sciences, Rabies virus, Organisms, Public Health, Environmental and Occupational Health, Biology and Life Sciences, lcsh:RA1-1270, 15. Life on land, Tropical Diseases, medicine.disease, biology.organism_classification, Virology, 030104 developmental biology, Vampire bat, Lyssavirus, Zoology
Abstract

Introduction In addition to the commonly accepted importance of the vampire bat in the maintenance and transmission of the rabies virus (RABV) in South America, RABV infection of other species is widely evidenced, challenging their role in the viral cycle. Methodology / Principles findings To identify the bioecological drivers of RABV circulation in neotropical bat communities, we conducted a molecular and serological survey on almost 1,000 bats from 30 species, and a 4-year longitudinal survey in two colonies of vampire bats in French Guiana. RABV was molecularly detected in a common vampire and in a frugivorous bat. The sequences corresponded to haematophagous bat-related strains and were close to viruses circulating in the Brazilian Amazon region. Species’ seroprevalence ranged from 0 to 20%, and the risk of seropositivity was higher in bats with a haematophagous diet, living in monospecific colonies and in dense forests. The longitudinal survey showed substantial temporal fluctuations, with individual waves of seroconversions and waning immunity. The high prevalences observed in bat communities, in most habitats and in species that do not share the same microhabitats and bioecological patterns, the temporal variations, and a rather short period of detectable antibodies as observed in recaptured vampires suggest (i) frequent exposure of animals, (ii) an ability of the infected host to control and eliminate the virus, (iii) more relaxed modes of exposure between bats than the commonly assumed infection via direct contact with saliva of infected animals, all of which should be further investigated. Conclusions / significance We hypothesize that RABV circulation in French Guiana is mainly maintained in the pristine forest habitats that may provide sufficient food resources to allow vampire bats, the main prevalent species, to survive and RABV to be propagated. However, on the forest edge and in disturbed areas, human activities may induce more insidious effects such as defaunation. One of the ecological consequences is the disappearance of resources for tertiary or secondary consumers. Populations of vampires may then shift to alternative resources such as cattle, domestic animals and humans. Therefore, a good forest status, allowing both a dilution effect in highly rich bat communities and the maintenance of large populations of medium-sized and large mammals used as prey by vampires, should prevent their migration to anthropized areas., Author Summary The vampire bat is known to be the main reservoir of the rabies virus (RABV) in South America. Nevertheless, other bat species are implicated in the cycle of the virus. Indeed, seven genus-specific rabies lineages have been described in insectivorous bats in Brazil. In French Guiana, we looked for the presence of the virus in a large number of bats, belonging to 30 different species. We found a high rate of seropositive animals, mainly haematophagous bats, and in those living in monospecific colonies and in forest habitats. We also monitored two colonies of vampire bats over a 4-year period and found that some animals became seropositive for the RABV, while others, after being seropositive, were able to become seronegative. These data first of all demonstrate that the virus widely circulates in bat communities with transmission occurring via direct saliva contact with broken skin and mucosa at the intra-specific level in vampire bat species. Exposure of other bat species, including those that do not share the same microhabitat, occurs in all forest strata through modes of transmission that have yet to be determined. Secondly, these animals seem to be exposed regularly, and most of them have a great ability to control and eliminate the virus. Third, these results suggest that pristine forest habitats provide sufficient food resources for the survival of vampire bats and propagation of RABV. In contrast, in disturbed habitats, where resources are decreasing, the vampires might have to shift to alternative resources such as cattle, domestic animals or even human beings. Altogether, the risk of rabies virus transmission may increase on the edge between forest and anthropized areas.

Published
2016
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8. Identification of lymphocytic choriomeningitis mammarenavirus in house mouse (Mus musculus, Rodentia) in French Guiana

Author

Christiane Bouchier, Damien Donato, Benoit de Thoisy, Vincent Lacoste, Sourakhata Tirera, François Catzeflis, Anne Lavergne, Association Kwata - Etude et protection de la nature [Guyane], Center for Research and Exploration in Space Science and Technology [GSFC] (CRESST), NASA Goddard Space Flight Center (GSFC), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), ANR-11-LABX-0010,DRIIHM / IRDHEI,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011), Laboratoire des Interactions Virus-Hôtes [Cayenne, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Biomics, Centre de Recherche et Innovation Technologique (CITECH), Institut Pasteur [Paris] (IP)-Institut Pasteur [Paris] (IP), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), This study was conducted within the 'BioViRo' program, supported by an 'Investissement d'Avenir' grant managed by Agence Nationale de la Recherche (CEBA, ref. ANR-10-LABX-25-01) and a European commission 'REGPOT-CT-2011-285837-STRonGer' grant within the FP7. Field work conducted by BdT was funded by the ViRUSES program, supported by European funds (FEDER) and assistance from Région Guyane and Direction Régionale pour la Recherche et la Technologie, the ZNIEFF Guyane (DEAL Guyane) program, the GUYAMAZON II program, and FC in Trois Palétuviers was funded by Réseau des Observatoires Hommes-Milieux (OHM-Oyapok APR 2013). High throughput sequencing was performed on the Genomics Platform, member of the 'France Génomique' consortium (ANR10-INBS-09-08), and we thank Magali Tichit for her technical assistance during this sequencing stage., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut Pasteur [Paris]-Institut Pasteur [Paris], École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)

Subjects
0301 basic medicine, Microbiology (medical), Rodent Diseases, Rodent, Mouse, Genome, Viral, Lymphocytic Choriomeningitis, Lymphocytic choriomeningitis, Microbiology, House mouse, 03 medical and health sciences, Mice, Phylogenetics, biology.animal, Genetics, medicine, Animals, Lymphocytic choriomeningitis virus, Molecular Biology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Phylogeny, Lymphocytic choriomeningitis mammarenavirus, biology, Phylogenetic tree, Strain (biology), medicine.disease, biology.organism_classification, Virology, [SDE.ES]Environmental Sciences/Environmental and Society, French Guiana, Complete sequence, 030104 developmental biology, Infectious Diseases, House mice, Metagenomics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Thirty-seven house mice (Mus musculus, Rodentia) caught in different localities in French Guiana were screened to investigate the presence of lymphocytic choriomeningitis mammarenavirus (LCMV). Two animals trapped in an urban area were found positive, hosting a new strain of LCMV, that we tentatively named LCMV " Comou ". The complete sequence was determined using a metagenomic approach. Phylogenetic analyses revealed that this strain is related to genetic lineage I composed of strains inducing severe disease in humans. These results emphasize the need for active surveillance in humans as well as in house mouse populations, which is a rather common rodent in French Guianese cities and settlements.

Published
2015
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9. Absence of correlation between ex vivo susceptibility to doxycycline and pfteQ–pfmdt gene polymorphism in French Guiana

Author

Lise Musset, Eric Legrand, Damien Donato, Marie Mura, Béatrice Volney, Sébastien Briolant, Stéphane Pelleau, Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Direction Interarmées du Service de Santé en Guyane, Institut de Recherche Biomédicale des Armées (IRBA), This study benefited from European commission grant REGPOT-CT-2011-285837-STRonGer within the FP7 program me and the French Ministry of Health (InVS agency, Paris), European Project: 285837,EC:FP7:REGPOT,FP7-REGPOT-2011-1,STRONGER(2011), Institut de Recherche des Armées, European Project : 285837, EC:FP7:REGPOT, FP7-REGPOT-2011-1, STRONGER(2011), and Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
Genetic Markers, Plasmodium falciparum, 030231 tropical medicine, Drug Resistance, Gene Dosage, Protozoan Proteins, Drug resistance, Real-Time Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Antimalarials, 03 medical and health sciences, 0302 clinical medicine, Parasitic Sensitivity Tests, parasitic diseases, medicine, Anti-malarial drug resistance, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Doxycycline, 0303 health sciences, Polymorphism, Genetic, biology, 030306 microbiology, Research, Molecular markers, Bayes Theorem, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, biology.organism_classification, medicine.disease, Virology, 3. Good health, Malaria, French Guiana, [SDV.SP] Life Sciences [q-bio]/Pharmaceutical sciences, Infectious Diseases, Parasitology, Genetic marker, Immunology, Gene polymorphism, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Ex vivo, medicine.drug
Abstract

International audience; Background: In French Guiana, doxycycline is used for both chemoprophylaxis and the treatment of malaria. The presence of isolates with reduced ex vivo susceptibility to doxycycline in French Guiana makes it critical to identify any genetic determinants contributing to the chemosusceptibility level of Plasmodium falciparum to doxycycline, such as pfmdt and pftetQ, which were recently identified as potential molecular markers in African isolates. Methods: A Bayesian statistical approach was used to define different ex vivo doxycycline phenotypes. The pfmdt and pftetQ gene copy numbers were quantified by quantitative real-time polymerase chain reaction in 129 P. falcipa-rum isolates collected between 2000 and 2010, and pftetQ, pfrps7, pfssurRNA, and pflsurRNA sequences were analysed after amplification by polymerase chain reaction. Results: PftetQ and pfmdt copy numbers were not associated with reduced susceptibility to doxycycline in P. falci-parum within French Guiana. Sequence analysis of the genes revealed five known single nucleotide polymorphisms. Three new SNPs were identified in the apicoplast ribosomal RNA long sub-unit (pflsurRNA): C740T, A1875C and A1875T. These polymorphisms were not associated with reduced chemosusceptibility to doxycycline. Conclusions: The present study does not validate pfmdt and pftetQ genes as molecular markers of decreased susceptibility to doxycycline in P. falciparum isolates in French Guiana.

Published
2015
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10. Maripa hantavirus in French Guiana: phylogenetic position and predicted spatial distribution of rodent hosts

Author

Anne Lavergne, Amandine Guidez, François Catzeflis, Olivier Brunaux, Sébastien Barrioz, Luc Clément, Vincent Lacoste, Séverine Matheus, Stéphane Guitet, Damien Donato, Benoit de Thoisy, and Jean-François Cornu

Subjects
Disease reservoir, Orthohantavirus, DNA, Complementary, 030231 tropical medicine, Zygodontomys brevicauda, Molecular Sequence Data, Zoology, Rodentia, Hantavirus Pulmonary Syndrome, Antibodies, Viral, Kidney, Rodent Diseases, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, Virology, Animals, Humans, Lung, Phylogeny, 030304 developmental biology, Hantavirus, Demography, Disease Reservoirs, 0303 health sciences, Hantavirus pulmonary syndrome, biology, Phylogenetic tree, Base Sequence, Geography, Ecology, Sequence Analysis, DNA, Articles, biology.organism_classification, French Guiana, Infectious Diseases, Oligoryzomys fulvescens, RNA, Viral, Parasitology, Bunyaviridae
Abstract

A molecular screening of wild-caught rodents was conducted in French Guiana, South America to identify hosts of the hantavirus Maripa described in 2008 in a hantavirus pulmonary syndrome (HPS) case. Over a 9-year period, 418 echimyids and murids were captured. Viral RNA was detected in two sigmodontine rodents, Oligoryzomys fulvescens and Zygodontomys brevicauda, trapped close to the house of a second HPS case that occurred in 2009 and an O. fulvescens close to the fourth HPS case identified in 2013. Sequences from the rodents had 96% and 97% nucleotide identity (fragment of S and M segments, respectively) with the sequence of the first human HPS case. Phylogenetic reconstruc-tions based on the complete sequence of the S segment show that Maripa virus is closely related to Rio Mamore hantavirus. Using environmental descriptors of trapping sites, including vegetation, landscape units, rain, and human disturbance, a maximal entropy-based species distribution model allowed for identification of areas of higher predicted occurrence of the two rodents, where emergence risks of Maripa virus are expected to be higher. Hantaviruses (Bunyaviridae) are distributed worldwide.

Published
2014

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