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1. Rodent-borne viruses in French Guiana

Author

Anne, Lavergne, Séverine, Matheus, François, Catzeflis, Damien, Donato, Vincent, Lacoste, and Benoit, de Thoisy

Abstract

Among mammals, rodents play a key role in the emergence of viral diseases. In French Guiana, with 36 rodent species recorded in various ecosystems (pristine forests, savannas, anthropized environments), some natural habitats today encounter anthropogenic perturbations that induce changes in community structure and population dynamics. These modifications are sometimes associated with the circulation and emergence of viral pathogens. For 10 years, investigations on the circulation of two rodent-borne viruses, Hantavirus and Mammarenavirus, are underway in rodent populations as well as in humans for hantavirus. These investigations identified viruses from both genera in their potential reservoirs and allow describing the most favourable habitats for the reservoirs of hantavirus where the risk of viral emergence may be higher. We suggest to investigate how anthropic perturbations in rodent communities can drive the emergence of viruses that are currently confined to a small scale and search for evidence of infection in the human population.

Published
2020

2. 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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3. 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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4. DNA Polymerase Sequences of New World Monkey Cytomegaloviruses: Another Molecular Marker with Which To Infer Platyrrhini Systematics

Author

Anne Lavergne, Jean-François Pouliquen, Samantha James, Damien Donato, Manuel Ruiz-García, 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), Ecole Doctorale 587 : Diversités, santé et développement en Amazonie (ED 587), Université de Guyane (UG), Pontificia universidad Javeriana, Cali, Département de Virologie - Department of Virology, Institut Pasteur [Paris] (IP), S.J. was supported by a grant from the Université de la Guyane, École Doctorale 587-Diversités, Santé et Développement en Amazonie, and by a grant from the Collectivité Territoriale de la Guyane. This study was funded by a European commission REGPOT-CT-2011-285837-STRonGer grant within the FP7 and an Investissement d'Avenir grant managed by the Agence Nationale de la Recherche (CEBA) (grant ANR-10-LABX-25-01). It was also supported by grants 1203-09-11239 (Colciencias) and 120108-E0102141 (Fondo para la Acción Ambiental) to M.R.-G., Warm thanks go to Benoît de Thoisy for providing NWM DNA samples from French Guiana., 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), and Institut Pasteur [Paris]

Subjects
0301 basic medicine, MESH: Monkey Diseases/epidemiology, [SDV]Life Sciences [q-bio], Cytomegalovirus, DNA-Directed DNA Polymerase, medicine.disease_cause, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Polymerase Chain Reaction, Monophyly, chemistry.chemical_compound, Molecular marker, MESH: DNA, Viral/genetics, MESH: Animals, Clade, MESH: Evolution, Molecular, Phylogeny, New World monkey, MESH: Phylogeny, MESH: DNA, Viral/isolation & purification, MESH: DNA-Directed DNA Polymerase/genetics, MESH: DNA, Viral/blood, biology, Phylogenetic tree, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Monkey Diseases, CMV, MESH: Monkey Diseases/virology, Platyrrhini, MESH: Polymerase Chain Reaction/methods, MESH: Viral Proteins/genetics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Cytomegalovirus/classification, MESH: Monkey Diseases/blood, Immunology, MESH: Platyrrhini/virology, Microbiology, MESH: Cytomegalovirus/enzymology, Evolution, Molecular, 03 medical and health sciences, MESH: Exodeoxyribonucleases/genetics, Viral Proteins, Phylogenetics, Virology, MESH: South America/epidemiology, evolution, medicine, Animals, MESH: Cytomegalovirus/genetics, New World monkeys, MESH: Central America/epidemiology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Central America, South America, biology.organism_classification, 030104 developmental biology, Exodeoxyribonucleases, chemistry, Genetic Diversity and Evolution, Evolutionary biology, Insect Science, DNA, Viral
Abstract

International audience; Over the past few decades, a large number of studies have identified herpesvirus sequences from many mammalian species around the world. Among the different nonhuman primate species tested so far for cytomegaloviruses (CMVs), only a few were from the New World. Seeking to identify CMV homologues in New World monkeys (NWMs), we carried out molecular screening of 244 blood DNA samples from 20 NWM species from Central and South America. Our aim was to reach a better understanding of their evolutionary processes within the Platyrrhini parvorder. Using PCR amplification with degenerate consensus primers targeting highly conserved amino acid motifs encoded by the herpesvirus DNA polymerase gene, we characterized novel viral sequences from 12 species belonging to seven genera representative of the three NWM families. BLAST searches, pairwise nucleotide and amino acid sequence comparisons, and phylogenetic analyses confirmed that they all belonged to the Cytomegalovirus genus. Previously determined host taxa allowed us to demonstrate a good correlation between the distinct monophyletic clades of viruses and those of the infected primates at the genus level. In addition, the evolutionary branching points that separate NWM CMVs were congruent with the divergence dates of their hosts at the genus level. These results significantly expand our knowledge of the host range of this viral genus and strongly support the occurrence of cospeciation between these viruses and their hosts. In this respect, we propose that NWM CMV DNA polymerase gene sequences may serve as reliable molecular markers with which to infer Platyrrhini phylogenetics.IMPORTANCE Investigating evolutionary processes between viruses and nonhuman primates has led to the discovery of a large number of herpesviruses. No study published so far on primate cytomegaloviruses has extensively studied New World monkeys (NWMs) at the subspecies, species, genus, and family levels. The present study sought to identify cytomegalovirus homologues in NWMs and to decipher their evolutionary relationships. This led us to characterize novel viruses from 12 of the 20 primate species tested, which are representative of the three NWM families. The identification of distinct viruses in these primates not only significantly expands our knowledge of the host range of this viral genus but also sheds light on its evolutionary history. Phylogenetic analyses and molecular dating of the sequences obtained support a virus-host coevolution.

Published
2018
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5. African Great Apes Are Naturally Infected with Roseoloviruses Closely Related to Human Herpesvirus 7

Author

Antoine Gessain, Damien Donato, Ernst J. Verschoor, Eric Nerrienet, Vincent Lacoste, Anne Lavergne, and Henk Niphuis

Subjects
Genotype, Hominidae, viruses, Molecular Sequence Data, Immunology, Roseolovirus Infections, Sequence Homology, Gorilla, Subspecies, Polymerase Chain Reaction, Microbiology, Viral Proteins, 03 medical and health sciences, Phylogenetics, Virology, biology.animal, Animals, Cluster Analysis, Phylogeny, 030304 developmental biology, Genetics, 0303 health sciences, biology, Phylogenetic tree, 030306 microbiology, Primate Diseases, Sequence Analysis, DNA, biology.organism_classification, Pan paniscus, Blood, Genetic Diversity and Evolution, Insect Science, Africa, DNA, Viral, Common chimpanzee, Roseolovirus
Abstract

Primates are naturally infected with herpesviruses. During the last 15 years, the search for homologues of human herpesviruses in nonhuman primates allowed the identification of numerous viruses belonging to the different herpesvirus subfamilies and genera. No simian homologue of human herpesvirus 7 (HHV7) has been reported to date. To investigate the putative existence of HHV7-like viruses in African great apes, we applied the consensus-degenerate hybrid oligonucleotide primers (CODEHOP) program-mediated PCR strategy to blood DNA samples from the four common chimpanzee subspecies ( Pan troglodytes verus , P. t. ellioti , P. t. troglodytes , and P. t. schweinfurthii ), pygmy chimpanzees ( Pan paniscus ), as well as lowland gorillas ( Gorilla gorilla gorilla ). This study led to the discovery of a novel roseolovirus close to HHV7 in each of these nonhuman primate species and subspecies. Generation of the partial glycoprotein B (1,111-bp) and full-length DNA polymerase (3,036/3,042-bp) gene sequences allowed the deciphering of their evolutionary relationships. Phylogenetic analyses revealed that HHV7 and its African great ape homologues formed well-supported monophyletic lineages whose topological resemblance to the host phylogeny is suggestive of virus-host codivergence. Notably, the evolutionary branching points that separate HHV7 from African great ape herpesvirus 7 are remarkably congruent with the dates of divergence of their hosts. Our study shows that African great apes are hosts of human herpesvirus homologues, including HHV7 homologues, and that the latter, like other DNA viruses that establish persistent infections, have cospeciated with their hosts. IMPORTANCE Human herpesviruses are known to possess simian homologues. However, surprisingly, none has been identified to date for human herpesvirus 7 (HHV7). This study is the first to describe simian homologues of HHV7. The extensive search performed on almost all African great ape species and subspecies, i.e., common chimpanzees of the four subspecies, bonobos, and lowland gorillas, has allowed characterization of a specific virus in each. Genetic characterization of the partial glycoprotein B and full-length DNA polymerase gene sequences, followed by their phylogenetic analysis and estimation of divergence times, has shed light on the evolutionary relationships of these viruses. In this respect, we conclusively demonstrate the cospeciation between these new viruses and their hosts and report cases of cross-species transmission between two common chimpanzee subspecies in both directions.

Published
2014
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6. Patawa Virus, a New Arenavirus Hosted by Forest Rodents in French Guiana

Author

Séverine Matheus, Anne Lavergne, François Catzeflis, Damien Donato, Benoit de Thoisy, Amandine Guidez, 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), Association Kwata - Etude et protection de la nature [Guyane], Centre National de Référence pour les Arbovirus - Laboratoire de Virologie [Cayenne, Guyane française] (CNR - laboratoire associé), 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 ViRUSES program, supported by European funds (FEDER) and assistance from Région Guyane and Direction Régionale pour la Recherche et la Technologie, and received a European commission 'REGPOT-CT-2011-285837-STRonGer' Grant within the FP7 and an 'Investissement d’Avenir' Grant managed by Agence Nationale de la Recherche (CEBA, Ref. ANR-10-LABX-25-01). Field work at Cacao was funded by Agence Nationale de la Recherche under contract 2006-SEST-20-01 attributed to Th. De Meeus., FC acknowledges the technical expertise of Michel Gillioz at the Geneva Natural History Museum for curating specimens with care., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-06-NEUR-0039,OlfLocalTrans,Traduction locale axonale et dendritique dans le développement et le renouvellement du système olfactif(2006), European Project: 285837,EC:FP7:REGPOT,FP7-REGPOT-2011-1,STRONGER(2011), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)

Subjects
Rodent Diseases, MESH: French Guiana/epidemiology, Rodent, viruses, Health, Toxicology and Mutagenesis, MESH: Arenaviridae Infections/epidemiology, Forests, MESH: Base Sequence, phylogeny, MESH: Rodent Diseases/epidemiology, Amazonia, biology.animal, Animals, Arenaviridae Infections, MESH: Animals, Sigmodontinae, MESH: Sigmodontinae/virology, arenavirus, MESH: Rodent Diseases/virology, Muridae, Arenavirus, Base Sequence, Oecomys, Ecology, biology, Amazon rainforest, MESH: Arenavirus/isolation & purification, rodent, MESH: Forests, biology.organism_classification, French Guiana, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Animal ecology, MESH: Arenaviridae Infections/veterinary
Abstract

International audience; Molecular screening of rodents from French Guiana has detected a new arenavirus, named ''Pata-wa,'' in two Oecomys species (Muridae, Sigmodontinae). Further investigations are needed to better understand the circulation of this virus in rodent and human populations and its public health impact.

Published
2014
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7. 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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8. 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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