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Tang A, Zhang J, Huang J, Deng Y, Wang D, Yu P, Zhao R, Wang Y, Chen Z, Zhang T, Li B. Decrypting the viral community in aerobic activated sludge reactors treating antibiotic production wastewater. WATER RESEARCH 2024; 265:122253. [PMID: 39167968 DOI: 10.1016/j.watres.2024.122253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/31/2024] [Accepted: 08/10/2024] [Indexed: 08/23/2024]
Abstract
Viruses are the most abundant yet understudied members that may influence microbial metabolism in activated sludge treating antibiotic production wastewater. This study comprehensively investigated virome community characteristics under the selection pressure of nine types and different concentrations of antibiotics using a metagenomics approach. Of the 15,514 total viral operational taxonomic units (tOTUs) recovered, only 37.5 % were annotated. Antibiotics altered the original viral community structure in activated sludge. The proportion of some pathogenic viral families, including Herpesviridae_like, increased significantly in reactors treating erythromycin production wastewater. In total, 16.5 % of the tOTUs were associated with two or more hosts. tOTUs rarely carried antibiotic resistance genes (ARGs), and the ARG types in the tOTUs did not match the ARGs carried by the bacterial hosts. This suggests that transduction contributes little to the horizontal ARG transfer. Auxiliary metabolic genes (AMGs) were prevalent in tOTUs, and those involved in folate biosynthesis were particularly abundant, indicating their potential to mitigate antibiotic-induced host damage. This study provides comprehensive insights into the virome community in activated sludge treating antibiotic production wastewater and sheds light on the potential role of viral AMGs in mitigating antibiotic-induced stress.
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Affiliation(s)
- Aixi Tang
- Key Laboratory of Microorganism Application and Risk Control, Ministry of Ecology and Environment, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jiayu Zhang
- Key Laboratory of Microorganism Application and Risk Control, Ministry of Ecology and Environment, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jin Huang
- Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Renxin Zhao
- Key Laboratory of Microorganism Application and Risk Control, Ministry of Ecology and Environment, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yulin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266000, China
| | - Zihan Chen
- Key Laboratory of Microorganism Application and Risk Control, Ministry of Ecology and Environment, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Bing Li
- Key Laboratory of Microorganism Application and Risk Control, Ministry of Ecology and Environment, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
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2
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Cortines JR, Bridges CM, Subramanian S, Schrad JR, Araújo GRS, Nunes GHP, Oliveira JDS, Essus VA, Abrahão JS, White S, Parent KN, Teschke C. Transition metals and oxidation reactions trigger stargate opening during the initial stages of the replicative cycle of the giant Tupanvirus. mBio 2024:e0219224. [PMID: 39324795 DOI: 10.1128/mbio.02192-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024] Open
Abstract
Tupanviruses, members of the family Mimiviridae, infect phagocytic cells. Particle uncoating begins inside the phagosome, with capsid opening via the stargate. The mechanism through which this opening takes place is unknown. Once phagocytized, metal ion flux control and ROS are induced to inactivate foreign particles, including viruses. Here, we studied the effect of iron ions, copper ions, and H2O2 on Tupanvirus particles. Such treatments induced stargate opening in vitro, as observed by different microscopy techniques. Metal-treated viruses were found to be non-infectious, leading to the hypothesis that stargate opening likely resulted in the release of the viral seed, which is required for infection initiation. To the best of our knowledge, this is the first description of a giant virus capsid morphological change induced by transition metals and H2O2, which may be important to describe new virulence factors and capsid uncoating mechanisms.
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Affiliation(s)
- Juliana R Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Charles M Bridges
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Sundharraman Subramanian
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Jason R Schrad
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Glauber R S Araújo
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel Henrique Pereira Nunes
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana Dos Santos Oliveira
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victor Alejandro Essus
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jônatas S Abrahão
- Department of Microbiology, Federal University of Minas Gerais, Institute of Biological Sciences, Belo Horizonte, Minas Gerais, Brazil
| | - Simon White
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Carolyn Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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3
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Moniruzzaman M, Erazo Garcia MP, Farzad R, Ha AD, Jivaji A, Karki S, Sheyn U, Stanton J, Minch B, Stephens D, Hancks DC, Rodrigues RAL, Abrahao JS, Vardi A, Aylward FO. Virologs, viral mimicry, and virocell metabolism: the expanding scale of cellular functions encoded in the complex genomes of giant viruses. FEMS Microbiol Rev 2023; 47:fuad053. [PMID: 37740576 PMCID: PMC10583209 DOI: 10.1093/femsre/fuad053] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023] Open
Abstract
The phylum Nucleocytoviricota includes the largest and most complex viruses known. These "giant viruses" have a long evolutionary history that dates back to the early diversification of eukaryotes, and over time they have evolved elaborate strategies for manipulating the physiology of their hosts during infection. One of the most captivating of these mechanisms involves the use of genes acquired from the host-referred to here as viral homologs or "virologs"-as a means of promoting viral propagation. The best-known examples of these are involved in mimicry, in which viral machinery "imitates" immunomodulatory elements in the vertebrate defense system. But recent findings have highlighted a vast and rapidly expanding array of other virologs that include many genes not typically found in viruses, such as those involved in translation, central carbon metabolism, cytoskeletal structure, nutrient transport, vesicular trafficking, and light harvesting. Unraveling the roles of virologs during infection as well as the evolutionary pathways through which complex functional repertoires are acquired by viruses are important frontiers at the forefront of giant virus research.
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Affiliation(s)
- Mohammad Moniruzzaman
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Maria Paula Erazo Garcia
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Roxanna Farzad
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Anh D Ha
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Abdeali Jivaji
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Sangita Karki
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Uri Sheyn
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Joshua Stanton
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Benjamin Minch
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Danae Stephens
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, United States
| | - Rodrigo A L Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Jonatas S Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg, VA 24061, United States
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4
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Ha AD, Moniruzzaman M, Aylward FO. Assessing the biogeography of marine giant viruses in four oceanic transects. ISME COMMUNICATIONS 2023; 3:43. [PMID: 37120676 PMCID: PMC10148842 DOI: 10.1038/s43705-023-00252-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales. We found that most viruses appeared to be prevalent in shallow waters (<150 m), and that viruses of the Mesomimiviridae (Imitervirales) and Prasinoviridae (Algavirales) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation genes that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.
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Affiliation(s)
- Anh D Ha
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA, 24061, USA
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA, 24061, USA.
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg, VA, 24061, USA.
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5
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Ha AD, Moniruzzaman M, Aylward FO. Assessing the biogeography of marine giant viruses in four oceanic transects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526306. [PMID: 36778472 PMCID: PMC9915497 DOI: 10.1101/2023.01.30.526306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales . We found that most viruses appeared to be prevalent in shallow waters (<150 meters), and that viruses of the Mesomimiviridae ( Imitervirales ) and Prasinoviridae ( Algavirales ) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.
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Affiliation(s)
- Anh D. Ha
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061
| | - Mohammad Moniruzzaman
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables FL 33149
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg VA, 24061
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6
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Giant Viruses as a Source of Novel Enzymes for Biotechnological Application. Pathogens 2022; 11:pathogens11121453. [PMID: 36558786 PMCID: PMC9787589 DOI: 10.3390/pathogens11121453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application.
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7
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Aylward FO, Moniruzzaman M. Viral Complexity. Biomolecules 2022; 12:1061. [PMID: 36008955 PMCID: PMC9405923 DOI: 10.3390/biom12081061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 12/18/2022] Open
Abstract
Although traditionally viewed as streamlined and simple, discoveries over the last century have revealed that viruses can exhibit surprisingly complex physical structures, genomic organization, ecological interactions, and evolutionary histories. Viruses can have physical dimensions and genome lengths that exceed many cellular lineages, and their infection strategies can involve a remarkable level of physiological remodeling of their host cells. Virus-virus communication and widespread forms of hyperparasitism have been shown to be common in the virosphere, demonstrating that dynamic ecological interactions often shape their success. And the evolutionary histories of viruses are often fraught with complexities, with chimeric genomes including genes derived from numerous distinct sources or evolved de novo. Here we will discuss many aspects of this viral complexity, with particular emphasis on large DNA viruses, and provide an outlook for future research.
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Affiliation(s)
- Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
| | - Mohammad Moniruzzaman
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Coral Gables, FL 33149, USA;
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8
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Brahim Belhaouari D, Pires De Souza GA, Lamb DC, Kelly SL, Goldstone JV, Stegeman JJ, Colson P, La Scola B, Aherfi S. Metabolic arsenal of giant viruses: Host hijack or self-use? eLife 2022; 11:e78674. [PMID: 35801640 PMCID: PMC9270025 DOI: 10.7554/elife.78674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/22/2022] [Indexed: 12/11/2022] Open
Abstract
Viruses generally are defined as lacking the fundamental properties of living organisms in that they do not harbor an energy metabolism system or protein synthesis machinery. However, the discovery of giant viruses of amoeba has fundamentally challenged this view because of their exceptional genome properties, particle sizes and encoding of the enzyme machinery for some steps of protein synthesis. Although giant viruses are not able to replicate autonomously and still require a host for their multiplication, numerous metabolic genes involved in energy production have been recently detected in giant virus genomes from many environments. These findings have further blurred the boundaries that separate viruses and living organisms. Herein, we summarize information concerning genes and proteins involved in cellular metabolic pathways and their orthologues that have, surprisingly, been discovered in giant viruses. The remarkable diversity of metabolic genes described in giant viruses include genes encoding enzymes involved in glycolysis, gluconeogenesis, tricarboxylic acid cycle, photosynthesis, and β-oxidation. These viral genes are thought to have been acquired from diverse biological sources through lateral gene transfer early in the evolution of Nucleo-Cytoplasmic Large DNA Viruses, or in some cases more recently. It was assumed that viruses are capable of hijacking host metabolic networks. But the giant virus auxiliary metabolic genes also may represent another form of host metabolism manipulation, by expanding the catalytic capabilities of the host cells especially in harsh environments, providing the infected host cells with a selective evolutionary advantage compared to non-infected cells and hence favoring the viral replication. However, the mechanism of these genes' functionality remains unclear to date.
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Affiliation(s)
- Djamal Brahim Belhaouari
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - David C Lamb
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
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9
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Aherfi S, Brahim Belhaouari D, Pinault L, Baudoin JP, Decloquement P, Abrahao J, Colson P, Levasseur A, Lamb DC, Chabriere E, Raoult D, La Scola B. Incomplete tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: is it still a virus? THE ISME JOURNAL 2022; 16:695-704. [PMID: 34556816 PMCID: PMC8857278 DOI: 10.1038/s41396-021-01117-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/24/2022]
Abstract
The discovery of Acanthamoeba polyphaga Mimivirus, the first isolated giant virus of amoeba, challenged the historical hallmarks defining a virus. Giant virion sizes are known to reach up to 2.3 µm, making them visible by optical microscopy. Their large genome sizes of up to 2.5 Mb can encode proteins involved in the translation apparatus. We have investigated possible energy production in Pandoravirus massiliensis. Mitochondrial membrane markers allowed for the detection of a membrane potential in purified virions and this was enhanced by a regulator of the tricarboxylic acid cycle but abolished by the use of a depolarizing agent. Bioinformatics was employed to identify enzymes involved in virion proton gradient generation and this approach revealed that eight putative P. massiliensis proteins exhibited low sequence identities with known cellular enzymes involved in the universal tricarboxylic acid cycle. Further, all eight viral genes were transcribed during replication. The product of one of these genes, ORF132, was cloned and expressed in Escherichia coli, and shown to function as an isocitrate dehydrogenase, a key enzyme of the tricarboxylic acid cycle. Our findings show for the first time that a membrane potential can exist in Pandoraviruses, and this may be related to tricarboxylic acid cycle. The presence of a proton gradient in P. massiliensis makes this virus a form of life for which it is legitimate to ask the question "what is a virus?".
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Affiliation(s)
- Sarah Aherfi
- Aix Marseille Univ, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Djamal Brahim Belhaouari
- Aix Marseille Univ, IRD, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Lucile Pinault
- Aix Marseille Univ, IRD, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Jean-Pierre Baudoin
- Aix Marseille Univ, IRD, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Philippe Decloquement
- Aix Marseille Univ, IRD, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Jonatas Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo, Horizonte, Brazil
| | - Philippe Colson
- Aix Marseille Univ, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix Marseille Univ, IRD, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - David C Lamb
- Faculty of Health and Life Sciences, Swansea University, Swansea, UK
| | - Eric Chabriere
- Aix Marseille Univ, IRD, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix Marseille Univ, IRD, MEPHI, Marseille, France.
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France.
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France.
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10
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Dos Santos Oliveira J, Lavell AA, Essus VA, Souza G, Nunes GHP, Benício E, Guimarães AJ, Parent KN, Cortines JR. Structure and physiology of giant DNA viruses. Curr Opin Virol 2021; 49:58-67. [PMID: 34051592 DOI: 10.1016/j.coviro.2021.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 02/02/2023]
Abstract
Although giant viruses have existed for millennia and possibly exerted great evolutionary influence in their environment. Their presence has only been noticed by virologists recently with the discovery of Acanthamoeba polyphaga mimivirus in 2003. Its virion with a diameter of 500 nm and its genome larger than 1 Mpb shattered preconceived standards of what a virus is and triggered world-wide prospection studies. Thanks to these investigations many giant virus families were discovered, each with its own morphological peculiarities and genomes ranging from 0.4 to 2.5 Mpb that possibly encode more than 400 viral proteins. This review aims to present the morphological diversity, the different aspects observed in host-virus interactions during replication, as well as the techniques utilized during their investigation.
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Affiliation(s)
- Juliana Dos Santos Oliveira
- Departamento de Virologia, Instituto de Mcirobiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21590-902, Rio de Janeiro, Brazil
| | - Anastasiya A Lavell
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Victor Alejandro Essus
- Departamento de Virologia, Instituto de Mcirobiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21590-902, Rio de Janeiro, Brazil
| | - Getúlio Souza
- Departamento de Virologia, Instituto de Mcirobiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21590-902, Rio de Janeiro, Brazil
| | - Gabriel Henrique Pereira Nunes
- Departamento de Virologia, Instituto de Mcirobiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21590-902, Rio de Janeiro, Brazil
| | - Eduarda Benício
- Departamento de Virologia, Instituto de Mcirobiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21590-902, Rio de Janeiro, Brazil
| | - Allan Jefferson Guimarães
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Brazil
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
| | - Juliana R Cortines
- Departamento de Virologia, Instituto de Mcirobiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21590-902, Rio de Janeiro, Brazil.
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11
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Mougari S, Chelkha N, Sahmi-Bounsiar D, Di Pinto F, Colson P, Abrahao J, La Scola B. A virophage cross-species infection through mutant selection represses giant virus propagation, promoting host cell survival. Commun Biol 2020; 3:248. [PMID: 32439847 PMCID: PMC7242381 DOI: 10.1038/s42003-020-0970-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/15/2020] [Indexed: 01/03/2023] Open
Abstract
Virus adaptation to new hosts is a major cause of infectious disease emergence. This mechanism has been intensively studied in the context of zoonotic virus spillover, due to its impact on global health. However, it remains unclear for virophages, parasites of giant viruses and potential regulators of microbial communities. Here, we present, for the first time to our knowledge, evidence of cross-species infection of a virophage. We demonstrated that challenging the native population of Guarani virophage with two previously unidentified giant viruses, previously nonpermissive to this virophage, allows the selection of a mutant genotype able to infect these giant viruses. We were able to characterize the potential genetic determinant (deletion) carried by the virophage with the expanded-host range. Our study also highlights the relevant biological impact of this host adaptation by demonstrating that coinfection with the mixture containing the mutant virophage abolishes giant virus production and rescues the host cell population from lysis.
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Affiliation(s)
- Said Mougari
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France.
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
| | - Nisrine Chelkha
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Dehia Sahmi-Bounsiar
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Fabrizio Di Pinto
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Colson
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Jonatas Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil, postal code 31270-901.
| | - Bernard La Scola
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France.
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
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12
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Schrad JR, Abrahão JS, Cortines JR, Parent KN. Structural and Proteomic Characterization of the Initiation of Giant Virus Infection. Cell 2020; 181:1046-1061.e6. [PMID: 32392465 DOI: 10.1016/j.cell.2020.04.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/07/2020] [Accepted: 04/17/2020] [Indexed: 12/26/2022]
Abstract
Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four infection intermediates in Samba virus (Mimivirus genus, lineage A) as visualized by cryoelectron microscopy (cryo-EM), cryoelectron tomography (cryo-ET), and scanning electron microscopy (SEM). Each of these four intermediates reflects similar morphology to a stage that occurs in vivo. We show that these genome release stages are conserved in other mimiviruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved among disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.
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Affiliation(s)
- Jason R Schrad
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jônatas S Abrahão
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Juliana R Cortines
- Department of Virology, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil.
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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13
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Rodrigues RAL, da Silva LCF, Abrahão JS. Translating the language of giants: translation-related genes as a major contribution of giant viruses to the virosphere. Arch Virol 2020; 165:1267-1278. [DOI: 10.1007/s00705-020-04626-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/25/2020] [Indexed: 12/21/2022]
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14
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Dos Santos Silva LK, Rodrigues RAL, Dos Santos Pereira Andrade AC, Hikida H, Andreani J, Levasseur A, La Scola B, Abrahão JS. Isolation and genomic characterization of a new mimivirus of lineage B from a Brazilian river. Arch Virol 2020; 165:853-863. [PMID: 32052196 DOI: 10.1007/s00705-020-04542-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/08/2020] [Indexed: 11/25/2022]
Abstract
Since its discovery, the first identified giant virus associated with amoebae, Acanthamoeba polyphaga mimivirus (APMV), has been rigorously studied to understand the structural and genomic complexity of this virus. In this work, we report the isolation and genomic characterization of a new mimivirus of lineage B, named "Borely moumouvirus". This new virus exhibits a structure and replicative cycle similar to those of other members of the family Mimiviridae. The genome of the new isolate is a linear double-strand DNA molecule of ~1.0 Mb, containing over 900 open reading frames. Genome annotation highlighted different translation system components encoded in the DNA of Borely moumouvirus, including aminoacyl-tRNA synthetases, translation factors, and tRNA molecules, in a distribution similar to that in other lineage B mimiviruses. Pan-genome analysis indicated an increase in the genetic arsenal of this group of viruses, showing that the family Mimiviridae is still expanding. Furthermore, phylogenetic analysis has shown that Borely moumouvirus is closely related to moumouvirus australiensis. This is the first mimivirus lineage B isolated from Brazilian territory to be characterized. Further prospecting studies are necessary for us to better understand the diversity of these viruses so a better classification system can be established.
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Affiliation(s)
- Ludmila Karen Dos Santos Silva
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | | | - Hiroyuki Hikida
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Julien Andreani
- Microbes, Evolution, Phylogeny and Infection (MEPHI), Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, 19-21 boulevard Jean moulin, 13005, Marseille, France
| | - Anthony Levasseur
- Microbes, Evolution, Phylogeny and Infection (MEPHI), Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, 19-21 boulevard Jean moulin, 13005, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France.
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, 19-21 boulevard Jean moulin, 13005, Marseille, France.
| | - Jônatas Santos Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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15
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Mougari S, Sahmi-Bounsiar D, Levasseur A, Colson P, La Scola B. Virophages of Giant Viruses: An Update at Eleven. Viruses 2019; 11:E733. [PMID: 31398856 PMCID: PMC6723459 DOI: 10.3390/v11080733] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/19/2022] Open
Abstract
The last decade has been marked by two eminent discoveries that have changed our perception of the virology field: The discovery of giant viruses and a distinct new class of viral agents that parasitize their viral factories, the virophages. Coculture and metagenomics have actively contributed to the expansion of the virophage family by isolating dozens of new members. This increase in the body of data on virophage not only revealed the diversity of the virophage group, but also the relevant ecological impact of these small viruses and their potential role in the dynamics of the microbial network. In addition, the isolation of virophages has led us to discover previously unknown features displayed by their host viruses and cells. In this review, we present an update of all the knowledge on the isolation, biology, genomics, and morphological features of the virophages, a decade after the discovery of their first member, the Sputnik virophage. We discuss their parasitic lifestyle as bona fide viruses of the giant virus factories, genetic parasites of their genomes, and then their role as a key component or target for some host defense mechanisms during the tripartite virophage-giant virus-host cell interaction. We also present the latest advances regarding their origin, classification, and definition that have been widely discussed.
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Affiliation(s)
- Said Mougari
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Dehia Sahmi-Bounsiar
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Colson
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France.
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France.
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005 Marseille, France.
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France.
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