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55. Old World Medieval Treponema pallidum Complex Treponematosis: A Case Report.

Author

Hama, Hamadou Oumarou, Boualam, Mahmoud A, Levasseur, Anthony, Ardagna, Yann, Adalian, Pascal, Chaix, Annie-Claire, and Drancourt, Michel

Subjects
TREPONEMA pallidum, GLOBUS pallidus, MEDICAL microbiology, COMMUNICABLE diseases, METAGENOMICS
Abstract

Background Introduction of 1 Treponema pallidum complex pathogen in naive European populations following the return of Christopher Columbus' troops from Central America in 1493 is a central dogma in venereology. Methods Among skeletal elements from the seventh or eighth century uncovered in Roquevaire, France, individual RS-1003 femur macroscopically suspected of having an infectious disease was investigated by means of paleoautoimmunohistochemistry, direct metagenomics, and paleoserology, along with 1 control femur from an apparently healthy individual (R-1003) and experimental negative controls. Results RS-1003 femur showed infectious bone; paleoautoimmunohistochemistry of the lesions led to microscopic detection of a T. pallidum complex pathogen. Phylogenetic analyses comprising 71 T. pallidum complex–specific reads covering 2.37% of the T. pallidum subsp. pallidum reference genome sequence revealed an ancestral T. pallidum complex pathogen in the lesion. Paleoserology detecting T. pallidum –specific antigens confirmed positive serological findings in individual RS-1003. Individual R-1003 and the negative controls remained negative. Conclusions This case, predating by 8 centuries previous detections of T. pallidum complex treponematosis in Europe, indicated that European populations were not naive to these pathogens before the 1493 introduction of a Central American T. pallidum complex pathogen overwhelming the T. pallidum ones previously circulating in the Old World. These data break a century-old dogma in medical microbiology. [ABSTRACT FROM AUTHOR]

Published
2023
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63. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

Author

Dhillon, Braham, Feau, Nicolas, Aerts, Andrea L., Beauseigle, Stéphanie, Bernier, Louis, Copeland, Alex, Foster, Adam, Gill, Navdeep, Henrissat, Bernard, Herath, Padmini, LaButti, Kurt M., Levasseur, Anthony, Lindquist, Erika A., Majoor, Eline, Ohm, Robin A., Pangilinan, Jasmyn L., Pribowo, Amadeus, Saddler, John N., Sakalidis, Monique L., de Vries, Ronald P., Grigoriev, Igor V., Goodwin, Stephen B., Tanguay, Philippe, and Hamelin, Richard C.

Published
2015

65. The emergence, spread and vanishing of a French SARS‐CoV‐2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule

Author

Colson, Philippe, primary, Gautret, Philippe, additional, Delerce, Jeremy, additional, Chaudet, Hervé, additional, Pontarotti, Pierre, additional, Forterre, Patrick, additional, Tola, Raphael, additional, Bedotto, Marielle, additional, Delorme, Léa, additional, Bader, Wahiba, additional, Levasseur, Anthony, additional, Lagier, Jean‐Christophe, additional, Million, Matthieu, additional, Yahi, Nouara, additional, Fantini, Jacques, additional, La Scola, Bernard, additional, Fournier, Pierre‐Edouard, additional, and Raoult, Didier, additional

Published
2022
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66. Genomic description and prevalence of two new Candidatus Saccharibacteria species from the human gut in different samples and countries

Author

Naud, Sabrina, primary, Caputo, Aurélia, additional, Anani, Hussein, additional, Ibrahim, Ahmad, additional, Levasseur, Anthony, additional, Million, Matthieu, additional, Bedotto, Marielle, additional, Diakite, Ami, additional, Dhiver, Catherine, additional, Dubourg, Grégory, additional, and Raoult, Didier, additional

Published
2022
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67. SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding: potential tool to finest genomic watch

Author

DUDOUET, Pierre, primary, COLSON, Philippe, additional, AHERFI, Sarah, additional, LEVASSEUR, Anthony, additional, BEYE, Mamadou, additional, DELERCE, Jeremy, additional, BUREL, Emilie, additional, LAVRARD, Philippe, additional, BADER, Wahiba, additional, LAGIER, Jean-Christophe, additional, FOURNIER, Pierre-Edouard, additional, SCOLA, Bernard LA, additional, and RAOULT, Didier, additional

Published
2022
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68. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Author

Riley, Robert, Salamov, Asaf A., Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitrios, Held, Benjamin W., Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika A., Sun, Hui, LaButti, Kurt M., Schmutz, Jeremy, Jabbour, Dina, Luoi, Hong, Baker, Scott E., Pisabarro, Antonio G., Walton, Jonathan D., Blanchette, Robert A., Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David S., and Grigoriev, Igor V.

Published
2014

71. Correction to: Description of Mediterraneibacter massiliensis, gen. nov., sp. nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., Mediterraneibacter lactaris comb. nov., Mediterraneibacter torques comb. nov., Mediterraneibacter gnavus comb. nov. and Mediterraneibacter glycyrrhizinilyticus comb. nov.

Author

Togo, Amadou Hamidou, Diop, Awa, Bittar, Fadi, Maraninchi, Marie, Valero, René, Armstrong, Nicholas, Dubourg, Grégory, Labas, Noémie, Richez, Magali, Delerce, Jeremy, Levasseur, Anthony, Fournier, Pierre-Edouard, Raoult, Didier, and Million, Matthieu

Published
2018
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72. Bartonella quintana Transmitted by Head Lice: An Outbreak of Trench Fever in Senegal.

Author

Hammoud, Alissa, Louni, Meriem, Fenollar, Florence, Bassene, Hubert, Sambou, Masse, Duclos, Nathalie, Diatta, Georges, Sokhna, Cheikh, Levasseur, Anthony, Raoult, Didier, and Mediannikov, Oleg

Subjects
PUBLIC health surveillance, MOLECULAR diagnosis, SEQUENCE analysis, DNA, GRAM-negative bacteria, DISEASE vectors, POINT-of-care testing, PEDICULOSIS, PUBLIC health, BLOOD collection, GENOMES, EPIDEMICS, DESCRIPTIVE statistics, RESEARCH funding, GRAM-negative bacterial diseases, POLYMERASE chain reaction, COLLECTION & preservation of biological specimens, INFECTIOUS disease transmission, DISEASE complications
Abstract

Background Louse-borne trench fever caused by Bartonella quintana is a neglected public health concern, known to be transmitted from body louse feces via scratching. No viable B. quintana have ever been isolated from head lice before; therefore, their role as a vector is still poorly understood. Methods In Senegal, the implementation of a permanent local surveillance system in a point-of-care laboratory (POC) allows the monitoring of emerging diseases. Here we used culture as well as molecular and genomic approaches to document an outbreak of trench fever associated with head lice in the village of Ndiop. Head lice and blood samples were collected from febrile patients between November 2010 and April 2015. Genomes of 2 isolated strains of B. quintana were sequenced and analyzed. Results A total of 2289 blood samples were collected in the 2010–2015 period. From 2010–2013, B. quintana DNA was detected by polymerase chain reaction (PCR) in 0.25% (4/1580). In 2014, 228 blood samples were collected, along with 161 head lice from 5 individuals. B. quintana DNA was detected in 4.4% (10/228) of blood samples, and in lice specimens collected from febrile patients (61.7%, 50/81) and non-febrile patients (61.4%, 43/70). Two B. quintana strains were isolated from blood and head lice from 2 different patients. Genomic sequence analysis showed 99.98% overall similarity between both strains. Conclusions The presence of live B. quintana in head lice, and the genetic identity of strains from patients' blood and head lice during a localized outbreak in Senegal, supports the evidence of head lice vectorial capacity. [ABSTRACT FROM AUTHOR]

Published
2023
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73. Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue

Author

Knauf, Sascha, Gogarten, Jan F., Schuenemann, Verena J., De Nys, Hélène M., Düx, Ariane, Strouhal, Michal, Mikalová, Lenka, Bos, Kirsten I., Armstrong, Roy, Batamuzi, Emmanuel K., Chuma, Idrissa S., Davoust, Bernard, Diatta, Georges, Fyumagwa, Robert D., Kazwala, Reuben R., Keyyu, Julius D., Lejora, Inyasi A. V., Levasseur, Anthony, Liu, Hsi, Mayhew, Michael A., Mediannikov, Oleg, Raoult, Didier, Wittig, Roman M., Roos, Christian, Leendertz, Fabian H., Šmajs, David, Nieselt, Kay, Krause, Johannes, and Calvignac-Spencer, Sébastien

Published
2018
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74. Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Zhang, Hua-Hao, Zhou, Qiu-Zhong, Wang, Ping-Lan, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Drezen, Jean-Michel, Béliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas E., Cheng, Peng-Fei, Han, Min-Jin, Zhang, Ze, Zhang, Xiao-Gu, and Dai, Fang-Yin

Published
2018
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76. MIMIVIRE is a defence system in mimivirus that confers resistance to virophage

Author

Levasseur, Anthony, Bekliz, Meriem, Chabriere, Eric, Pontarotti, Pierre, La Scola, Bernard, and Raoult, Didier

Subjects
DNA viruses -- Health aspects, Host-virus relationships -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Since their discovery, giant viruses have revealed several unique features that challenge the conventional definition of a virus, such as their large and complex genomes, their infection by virophages and [...]

Published
2016

80. Screening and Whole Genome Sequencing of SARS-CoV-2 Circulating During the First Three Waves of the COVID-19 Pandemic in Libreville and the Haut-Ogooué Province in Gabon

Author

Lekana-Douki, Sonia Etenna, primary, N'dilimabaka, Nadine, additional, Levasseur, Anthony, additional, Colson, Philippe, additional, Andeko, Julia Cyrielle, additional, Zong Minko, Ornella, additional, Banga Mve-Ella, Octavie, additional, Fournier, Pierre-Edouard, additional, Devaux, Christian, additional, Ondo, Bertrand Mve, additional, Akombi, Falone Larissa, additional, Yacka Mouele Bolo, Laurianne, additional, Ngonga Dikongo, Audrey Michel, additional, Diané, Abdoulaye, additional, Mabika Mabika, Arsène, additional, Mathouet, Jenny Francine, additional, Dzembo, Cresh, additional, Atiga, Nick Chenis, additional, Mouity Matoumba, Anicet, additional, Ndjangangoye, Nal Kennedy, additional, Bréchard, Ludivine, additional, Bedotto-Buffet, Marielle, additional, Mangombi Pambou, Joa Braithe, additional, Kandet Yattara, Marisca, additional, Mbongo Nkama, Elvire Anita, additional, Mintsa Ndong, Armel, additional, Adegnika, Ayola Akim, additional, Raoult, Didier, additional, Fenollar, Florence, additional, and Lekana-Douki, Jean-Bernard, additional

Published
2022
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81. Culture and identification of a “Deltamicron” SARS‐CoV‐2 in a three cases cluster in southern France

Author

Colson, Philippe, primary, Fournier, Pierre‐Edouard, additional, Delerce, Jeremy, additional, Million, Matthieu, additional, Bedotto, Marielle, additional, Houhamdi, Linda, additional, Yahi, Nouara, additional, Bayette, Jeremy, additional, Levasseur, Anthony, additional, Fantini, Jacques, additional, Raoult, Didier, additional, and La Scola, Bernard, additional

Published
2022
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82. Antiviral Activity of Repurposing Ivermectin against a Panel of 30 Clinical SARS-CoV-2 Strains Belonging to 14 Variants

Author

Delandre, Océane, primary, Gendrot, Mathieu, additional, Jardot, Priscilla, additional, Le Bideau, Marion, additional, Boxberger, Manon, additional, Boschi, Céline, additional, Fonta, Isabelle, additional, Mosnier, Joel, additional, Hutter, Sébastien, additional, Levasseur, Anthony, additional, La Scola, Bernard, additional, and Pradines, Bruno, additional

Published
2022
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83. Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics

Author

Colson, Philippe, Fournier, Pierre-Edouard, Chaudet, Hervé, Delerce, Jérémy, Giraud-Gatineau, Audrey, Houhamdi, Linda, Andrieu, Claudia, Brechard, Ludivine, Bedotto, Marielle, Prudent, Elsa, Gazin, Céline, Beye, Mamadou, Burel, Emilie, Dudouet, Pierre, Tissot-Dupont, Hervé, Gautret, Philippe, Lagier, Jean-Christophe, Million, Matthieu, Brouqui, Philippe, Parola, Philippe, Fenollar, Florence, Drancourt, Michel, La Scola, Bernard, Levasseur, Anthony, Raoult, Didier, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), 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), and ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, SARS-CoV-2, viruses, zoonosis, pandemics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, epidemics, variant, classification, [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, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, mutant, travel
Abstract

International audience; After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

Published
2022

84. Running Title: Cross-species multi-omics and conserved gene regulations

Author

Miyauchi, Shingo, Hage, Hayat, Drula, Elodie, Lesage-Meessen, Laurence, Berrin, Jean-Guy, Navarro, David, Favel, Anne, Chaduli, Delphine, Grisel, Sacha, Haon, Mireille, Piumi, François, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, Barry, Kerrie, LaButti, Kurt M, Chevret, Didier, Daum, Chris, Mariette, Jérôme, Klopp, Christophe, Cullen, Daniel, de Vries, Ronald P, Gathman, Allen C, Hainaut, Matthieu, Henrissat, Bernard, Hildén, Kristiina S, Kües, Ursula, Lilly, Walt, Lipzen, Anna, Mäkelä, Miia R, Martinez, Angel T, Morel-Rouhier, Mélanie, Morin, Emmanuelle, Pangilinan, Jasmyn, Ram, Arthur F J, Wösten, Han A B, Ruiz-Dueñas, Francisco J, Riley, Robert, Record, Eric, Grigoriev, Igor V, Rosso, Marie-Noëlle, Molecular Microbiology, Sub Molecular Plant Physiology, Sub Molecular Microbiology, Molecular Plant Physiology, Department of Microbiology, Department of Food and Nutrition, Fungal Genetics and Biotechnology, Helsinki Institute of Sustainability Science (HELSUS), Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), U.S. Department of Energy [Washington] (DOE), 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 Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), USDA Forest Service Rocky Mountain Forest and Range Experiment Station, United States Department of Agriculture (USDA), Westerdijk Fungal Biodiversity Institute [Utrecht] (WI), Royal Netherlands Academy of Arts and Sciences (KNAW), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Missouri Southern State University (MSSU), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Molecular Cell Biology [Göttingen], Max Planck Institute for Biophysical Chemistry (MPI-BPC), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), DOE Joint Genome Institute [Walnut Creek], Department of Molecular Microbiology and Biotechnology, Tel Aviv University (TAU), Utrecht University [Utrecht], Department of Plant Pathology & Microbiology [Riverside], University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231Ministerio de Ciencias, Innovación y Universidades de España (BIO2017-86559-R), ANR-14-CE06-0020,FUNTUNE,Cocktails enzymatiques inspirés de modèles fongiques pour la déconstruction contrôlée de la biomasse végétale(2014), Molecular Microbiology, Sub Molecular Plant Physiology, Sub Molecular Microbiology, Molecular Plant Physiology, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Westerdijk Fungal Biodiversity Insitute [Utrecht] (WI), University of Helsinki, Tel Aviv University [Tel Aviv], University of California [Riverside] (UCR), University of California-University of California, COMBE, Isabelle, Appel à projets générique - Cocktails enzymatiques inspirés de modèles fongiques pour la déconstruction contrôlée de la biomasse végétale - - FUNTUNE2014 - ANR-14-CE06-0020 - Appel à projets générique - VALID, Agence Nationale de la Recherche (France), Department of Energy (US), Ministerio de Ciencia, Innovación y Universidades (España), Miyauchi, Shingo [0000-0002-0620-5547], Hage, Hayat [0000-0003-4118-1816], Drula, Elodie [0000-0002-9168-5214], Lesage-Meessen, Laurence [0000-0003-2275-2978], Berrin, Jean-Guy [0000-0001-7570-3745], Navarro, David [0000-0002-3266-8270], Favel, Anne [0000-0003-2255-3637], Haon, Mireille [0000-0002-5669-5177], Levasseur, Anthony [0000-0003-2989-7539], Lomascolo, Anne [0000-0003-3829-8503], Ahrendt, Steven [0000-0002-3029-2126], LaButti, Kurt M. [0000-0002-5838-1972], Chevret, Didier [0000-0001-9531-7657], Daum, Chris [0000-0003-3895-5892], Klopp, Christophe [0000-0001-7126-5477], Vries, Ronald P. de [0000-0002-4363-1123], Hainaut, Matthieu [0000-0002-7567-657X], Henrissat, Bernard [0000-0002-3434-8588], Hildén, Kristiina S. [0000-0002-0126-8186], Kües, Ursula [0000-0001-9180-4079], Lipzen, Anna [0000-0003-2293-9329], Mäkelä, Miia [0000-0003-0771-2329], Martínez, Ángel T. [0000-0002-1584-2863], Morel-Rouhier, Mélanie [0000-0001-5149-0474], Morin, Emmanuelle [0000-0002-7268-972X], Ram, Arthur [0000-0002-2487-8016], Wösten, Han [0000-0002-0399-3648], Ruiz-Dueñas, F. J. [0000-0002-9837-5665], Record, Éric [0000-0002-7545-9997], Grigoriev, Igor V. [0000-0002-3136-8903], Rosso, Marie-Noëlle [0000-0001-8317-7220], Miyauchi, Shingo, Hage, Hayat, Drula, Elodie, Lesage-Meessen, Laurence, Berrin, Jean-Guy, Navarro, David, Favel, Anne, Haon, Mireille, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, LaButti, Kurt M., Chevret, Didier, Daum, Chris, Klopp, Christophe, Vries, Ronald P. de, Hainaut, Matthieu, Henrissat, Bernard, Hildén, Kristiina S., Kües, Ursula, Lipzen, Anna, Mäkelä, Miia, Martínez, Ángel T., Morel-Rouhier, Mélanie, Morin, Emmanuelle, Ram, Arthur, Wösten, Han, Ruiz-Dueñas, F. J., Record, Éric, Grigoriev, Igor V., and Rosso, Marie-Noëlle

Subjects
AcademicSubjects/SCI01140, SELECTION, Cellobiose, Lignin, ANNOTATION, chemistry.chemical_compound, lignocellulose, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Phylogeny, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 11832 Microbiology and virology, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Genome, Full Paper, Basidiomycota, General Medicine, PHANEROCHAETE-CHRYSOSPORIUM, Wood, Pycnoporus, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, GENOME, Fungal, Biochemistry, CAZyme, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lytic polysaccharide monooxygenase, Genome, Fungal, ENZYMES, CAZymes, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Biotechnology, DATABASE, 1.1 Normal biological development and functioning, Plant Biology & Botany, AcademicSubjects/MED00774, Biology, CLASSIFICATION, Fungal Proteins, CERIPORIOPSIS-SUBVERMISPORA, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Underpinning research, Oxidative enzyme, Genetics, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Cellulose, Molecular Biology, Gene, 030304 developmental biology, Lytic Polysaccharide Monooxygenase (LPMO), Comparative genomics, Lytic Polysaccharide Monooxygenase, 030306 microbiology, 15. Life on land, DEGRADATION, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, chemistry, Class II Peroxidase, wood decay, Carbohydrate Dehydrogenases, SECRETOME, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

14 p.-8 fig.-1 tab., White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here we combined comparative genomics,transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood decaying activity within the Basidiomycota genus Pycnoporus. We observed strong conservation in the genome structures and the repertoires of protein coding genes across the four Pycnoporus species described to date,despite the species having distinct geographic distributions. We further analyzed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin.The co-occurrence in the exo-proteomes of H2O2 producing enzymes with H2O2 consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 LPMO gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood decaying process., This work was supported by The French National Agency for Research (ANR-14-CE06-0020). The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The work by CSIC was supported by the Ministerio de Ciencias, Innovación y Universidades de España (BIO2017-86559-R).

Published
2020

85. The emergence, spread and vanishing of a French SARS‐CoV‐2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule.

Author

Colson, Philippe, Gautret, Philippe, Delerce, Jeremy, Chaudet, Hervé, Pontarotti, Pierre, Forterre, Patrick, Tola, Raphael, Bedotto, Marielle, Delorme, Léa, Bader, Wahiba, Levasseur, Anthony, Lagier, Jean‐Christophe, Million, Matthieu, Yahi, Nouara, Fantini, Jacques, La Scola, Bernard, Fournier, Pierre‐Edouard, and Raoult, Didier

Subjects
SARS-CoV-2, RNA viruses, EPIDEMICS, NUCLEOTIDE sequencing, DEATH rate
Abstract

The nature and dynamics of mutations associated with the emergence, spread, and vanishing of SARS‐CoV‐2 variants causing successive waves are complex. We determined the kinetics of the most common French variant ("Marseille‐4") for 10 months since its onset in July 2020. Here, we analyzed and classified into subvariants and lineages 7453 genomes obtained by next‐generation sequencing. We identified two subvariants, Marseille‐4A, which contains 22 different lineages of at least 50 genomes, and Marseille‐4B. Their average lifetime was 4.1 ± 1.4 months, during which 4.1 ± 2.6 mutations accumulated. Growth rate was 0.079 ± 0.045, varying from 0.010 to 0.173. Most of the lineages exhibited a bell‐shaped distribution. Several beneficial mutations at unpredicted sites initiated a new outbreak, while the accumulation of other mutations resulted in more viral heterogenicity, increased diversity and vanishing of the lineages. Marseille‐4B emerged when the other Marseille‐4 lineages vanished. Its ORF8 gene was knocked out by a stop codon, as reported in SARS‐CoV‐2 of mink and in the Alpha variant. This subvariant was associated with increased hospitalization and death rates, suggesting that ORF8 is a nonvirulence gene. We speculate that the observed heterogenicity of a lineage may predict the end of the outbreak. [ABSTRACT FROM AUTHOR]

Published
2023
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86. First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France

Author

Colson, Philippe, primary, Delerce, Jérémy, additional, Beye, Mamadou, additional, Levasseur, Anthony, additional, Boschi, Céline, additional, Houhamdi, Linda, additional, Tissot‐Dupont, Hervé, additional, Yahi, Nouara, additional, Million, Matthieu, additional, La Scola, Bernard, additional, Fantini, Jacques, additional, Raoult, Didier, additional, and Fournier, Pierre‐Edouard, additional

Published
2022
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87. Introduction of the SARS-CoV-2 Beta variant from Comoros into the Marseille geographical area

Author

Hoang, Van Thuan, primary, Assoumani, Loutfia, additional, Delerce, Jérémy, additional, Houhamdi, Linda, additional, Bedotto, Marielle, additional, Lagier, Jean-Christophe, additional, Million, Matthieu, additional, Levasseur, Anthony, additional, Fournier, Pierre-Edouard, additional, La Scola, Bernard, additional, Raoult, Didier, additional, Gautret, Philippe, additional, and Colson, Philippe, additional

Published
2022
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88. The emergence, spread and vanishing of a French SARS-CoV-2 variant exemplifies the fate of RNA virus epidemics and obeys the Black Queen rule

Author

Colson, Philippe, primary, Gautret, philippe, additional, Delerce, Jeremy, additional, Chaudet, Herve, additional, Pontarotti, Pierre, additional, Forterre, Patrick, additional, Tola, Raphael, additional, Bedotto, Marielle, additional, Delorme, Lea, additional, LEVASSEUR, Anthony, additional, Lagier, Jean-Christophe, additional, Million, Matthieu, additional, Yahi, Nouara, additional, Fantini, Jacques, additional, La Scola, Bernard, additional, Fournier, Pierre-Edouard, additional, and Raoult, Didier, additional

Published
2022
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89. Epidemiology and genomic characterisation of travel-associated and locally-acquired influenza, Marseille, France

Author

Dao, Thi Loi, primary, Levasseur, Anthony, additional, Tall, Mamadou Lamine, additional, Hoang, Van Thuan, additional, Colson, Philippe, additional, Caputo, Aurélia, additional, Ly, Tran Duc Anh, additional, Ninove, Laetitia, additional, Grimaldier, Clio, additional, Jardot, Priscilla, additional, Marty, Pierre, additional, La Scola, Bernard, additional, and Gautret, Philippe, additional

Published
2022
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92. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen

Author

DiGuistini, Scott, Wang, Ye, Liao, Nancy Y., Taylor, Greg, Tanguay, Philippe, Feau, Nicolas, Henrissat, Bernard, Chan, Simon K., Hesse-Orce, Uljana, Alamouti, Sepideh Massoumi, Tsui, Clement K. M., Docking, Roderick T., Levasseur, Anthony, Haridas, Sajeet, Robertson, Gordon, Birol, Inanc, Holt, Robert A., Marra, Marco A., Hamelin, Richard C., Hirst, Martin, Jones, Steven J. M., Bohlmann, Jörg, Breuil, Colette, and Croteau, Rodney B.

Published
2011

93. Full-length title: Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection

Author

Colson, Philippe, Dhiver, Catherine, Tamalet, Catherine, Delerce, Jeremy, Glazunova, Olga O., Gaudin, Maxime, Levasseur, Anthony, and Raoult, Didier

Subjects
Retrovirus, lcsh:R, Tryptophan, virus diseases, lcsh:Medicine, HIV Infections, Genome, Viral, Virus Replication, Publisher Correction, Article, Gastrointestinal Microbiome, Cytidine Deaminase, DNA, Viral, HIV Seropositivity, Mutation, Codon, Terminator, HIV-1, Humans, Female, lcsh:Q, APOBEC Deaminases, Infection, lcsh:Science
Abstract

Strategies to cure HIV-infected patients by virus-targeting drugs have failed to date. We identified a HIV-1-seropositive woman who spontaneously suppressed HIV replication and had normal CD4-cell counts, no HIV-disease, no replication-competent virus and no cell HIV DNA detected with a routine assay. We suspected that dramatic HIV DNA degradation occurred post-infection. We performed multiple nested-PCRs followed by Sanger sequencing and applied a multiplex-PCR approach. Furthermore, we implemented a new technique based on two hybridization steps on beads prior to next-generation sequencing that removed human DNA then retrieved integrated HIV sequences with HIV-specific probes. We assembled ≈45% of the HIV genome and further analyzed the G-to-A mutations putatively generated by cellular APOBEC3 enzymes that can change tryptophan codons into stop codons. We found more G-to-A mutations in the HIV DNA from the woman than in that of her transmitting partner. Moreover, 74% of the tryptophan codons were changed to stop codons (25%) or were deleted as a possible consequence of gene inactivation. Finally, we found that this woman’s cells remained HIV-susceptible in vitro. Our findings show that she does not exhibit innate HIV-resistance but may have been cured of it by extrinsic factors, a plausible candidate for which is the gut microbiota.

Published
2020

95. Pneumococcal pneumonia among shipyard workers: Inside the features of disease onset

Author

Cassir, Nadim, Luciani, Léa, Ferrieux, David, Levasseur, Anthony, Fournier, Pierre-Edouard, Parola, Philippe, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [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, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

99. Clinical outcomes in patients infected with different SARS-CoV-2 variants at one hospital during three phases of the COVID-19 epidemic in Marseille, France

Author

Hoang, Van-Thuan, primary, Colson, Philippe, additional, Levasseur, Anthony, additional, Delerce, Jérémy, additional, Lagier, Jean-Christophe, additional, Parola, Philippe, additional, Million, Matthieu, additional, Fournier, Pierre-Edouard, additional, Raoult, Didier, additional, and Gautret, Philippe, additional

Published
2021
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100. Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution

Author

Devaux, Christian, Pinault, Lucile, Delerce, Jérémy, Raoult, Didier, Levasseur, Anthony, Frutos, Roger, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Centre National de la Recherche Scientifique (CNRS), 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), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, SARS-CoV-2, viruses, fungi, COVID-19, ACE2, COVID-19 vaccines, Review, Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [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, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, NRP-1, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, variant viruses, mink coronavirus
Abstract

International audience; The rapid spread of SARS-CoV-2 variants has quickly spanned doubts and the fear about their ability escape vaccine protection. Some of these variants initially identified in caged were also found in humans. The claim that these variants exhibited lower susceptibility to antibody neutralization led to the slaughter of 17 million minks in Denmark. SARS-CoV-2 prevalence tests led to the discovery of infected farmed minks worldwide. In this study, we revisit the issue of the circulation of SARS-CoV-2 variants in minks as a model of sarbecovirus interspecies evolution by: (1) comparing human and mink angiotensin I converting enzyme 2 (ACE2) and neuropilin 1 (NRP-1) receptors; (2) comparing SARS-CoV-2 sequences from humans and minks; (3) analyzing the impact of mutations on the 3D structure of the spike protein; and (4) predicting linear epitope targets for immune response. Mink-selected SARS-CoV-2 variants carrying the Y453F/D614G mutations display an increased affinity for human ACE2 and can escape neutralization by one monoclonal antibody. However, they are unlikely to lose most of the major epitopes predicted to be targets for neutralizing antibodies. We discuss the consequences of these results for the rational use of SARS-CoV-2 vaccines.

Published
2021

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