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Upadhyay M, Nair D, Moseley GW, Srivastava S, Kondabagil K. Giant Virus Global Proteomics Innovation: Comparative Evaluation of In-Gel and In-Solution Digestion Methods. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:170-181. [PMID: 38621149 DOI: 10.1089/omi.2024.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
With their unusually large genome and particle sizes, giant viruses (GVs) defy the conventional definition of viruses. Although most GVs isolated infect unicellular protozoans, such as amoeba, studies in the last decade have established their much wider prevalence infecting most eukaryotic supergroups and some giant viral families with the potential to be human pathogens. Their complexity, almost autonomous life cycle, and enigmatic evolution necessitate the study of GVs. The accurate assessment of GV proteome is a veritable challenge. We have compared the coverage of global protein identification using different methods for GVs isolated in Mumbai, Mimivirus Bombay (MVB), Powai Lake Megavirus (PLMV), and Kurlavirus (KV), along with two previously studied GVs, Acanthamoeba polyphaga Mimivirus (APMV) and Marseillevirus (MV). Our study shows that the simultaneous use of in-gel and in-solution digestion methods can significantly increase the coverage of protein identification in the global proteome analysis of purified GV particles. Combining the two methods of analyses, we identified an additional 72 proteins in APMV and 114 in MV compared with what have been previously reported. Similarly, proteomes of MVB, PLMV, and KV were analyzed, and a total of 242 proteins in MVB, 287 proteins in PLMV, and 174 proteins in KV were identified. Our results suggest that a combined methodology of in-gel and in-solution methods is more efficient and opens up new avenues for innovation in global proteome analysis of GVs. Future planetary health research on GVs can benefit from consideration of a broader range of proteomics methodologies as illustrated by the present study.
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Affiliation(s)
- Monica Upadhyay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Gregory W Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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2
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Morimoto D, Tateishi N, Takahashi M, Nagasaki K. Isolation of viruses, including mollivirus, with the potential to infect Acanthamoeba from a Japanese warm temperate zone. PLoS One 2024; 19:e0301185. [PMID: 38547190 PMCID: PMC10977731 DOI: 10.1371/journal.pone.0301185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
Acanthamoeba castellanii is infected with diverse nucleocytoplasmic large DNA viruses. Here, we report the co-isolation of 12 viral strains from marine sediments in Uranouchi Inlet, Kochi, Japan. Based on the morphological features revealed by electron microscopy, these isolates were classified into four viral groups including Megamimiviridae, Molliviridae, Pandoraviridae, and Pithoviridae. Genomic analyses indicated that these isolates showed high similarities to the known viral genomes with which they are taxonomically clustered, and their phylogenetic relationships were also supported by core gene similarities. It is noteworthy that Molliviridae was isolated from the marine sediments in the Japanese warm temperate zone because other strains have only been found in the subarctic region. Furthermore, this strain has 19 and 4 strain-specific genes found in Mollivirus sibericum and Mollivirus kamchatka, respectively. This study extends our knowledge about the habitat and genomic diversity of Molliviridae.
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Affiliation(s)
- Daichi Morimoto
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
| | - Naohisa Tateishi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | | | - Keizo Nagasaki
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
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3
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Yang XT, Wang J, Jiang YH, Zhang L, Du L, Li J, Liu F. Insight into the mechanism of gallstone disease by proteomic and metaproteomic characterization of human bile. Front Microbiol 2023; 14:1276951. [PMID: 38111640 PMCID: PMC10726133 DOI: 10.3389/fmicb.2023.1276951] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/16/2023] [Indexed: 12/20/2023] Open
Abstract
Introduction Cholesterol gallstone disease is a prevalent condition that has a significant economic impact. However, the role of the bile microbiome in its development and the host's responses to it remain poorly understood. Methods In this study, we conducted a comprehensive analysis of microbial and human bile proteins in 40 individuals with either gallstone disease or gallbladder polyps. We employed a combined proteomic and metaproteomic approach, as well as meta-taxonomic analysis, functional pathway enrichment, and Western blot analyses. Results Our metaproteomic analysis, utilizing the lowest common ancestor algorithm, identified 158 microbial taxa in the bile samples. We discovered microbial taxa that may contribute to gallstone formation, including β-glucuronidase-producing bacteria such as Streptococcus, Staphylococcus, and Clostridium, as well as those involved in biofilm formation like Helicobacter, Cyanobacteria, Pseudomonas, Escherichia coli, and Clostridium. Furthermore, we identified 2,749 human proteins and 87 microbial proteins with a protein false discovery rate (FDR) of 1% and at least 2 distinct peptides. Among these proteins, we found microbial proteins crucial to biofilm formation, such as QDR3, ompA, ndk, pstS, nanA, pfIB, and dnaK. Notably, QDR3 showed a gradual upregulation from chronic to acute cholesterol gallstone disease when compared to polyp samples. Additionally, we discovered other microbial proteins that enhance bacterial virulence and gallstone formation by counteracting host oxidative stress, including sodB, katG, rbr, htrA, and ahpC. We also identified microbial proteins like lepA, rtxA, pckA, tuf, and tpiA that are linked to bacterial virulence and potential gallstone formation, with lepA being upregulated in gallstone bile compared to polyp bile. Furthermore, our analysis of the host proteome in gallstone bile revealed enhanced inflammatory molecular profiles, including innate immune molecules against microbial infections. Gallstone bile exhibited overrepresented pathways related to blood coagulation, folate metabolism, and the IL-17 pathway. However, we observed suppressed metabolic activities, particularly catabolic metabolism and transport activities, in gallstone bile compared to polyp bile. Notably, acute cholelithiasis bile demonstrated significantly impaired metabolic activities compared to chronic cholelithiasis bile. Conclusion Our study provides a comprehensive metaproteomic analysis of bile samples related to gallstone disease, offering new insights into the microbiome-host interaction and gallstone formation mechanism.
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Affiliation(s)
- Xue-Ting Yang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
| | - Jie Wang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
| | - Ying-Hua Jiang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
| | - Lei Zhang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
| | - Ling Du
- Key Laboratory of Digestive Cancer Full Cycle Monitoring and Precise Intervention of Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, Shanghai, China
| | - Jun Li
- Department of Surgery, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Feng Liu
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
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Tokarz-Deptuła B, Chrzanowska S, Gurgacz N, Stosik M, Deptuła W. Virophages-Known and Unknown Facts. Viruses 2023; 15:1321. [PMID: 37376621 DOI: 10.3390/v15061321] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
The paper presents virophages, which, like their host, giant viruses, are "new" infectious agents whose role in nature, including mammalian health, is important. Virophages, along with their protozoan and algal hosts, are found in fresh inland waters and oceanic and marine waters, including thermal waters and deep-sea vents, as well as in soil, plants, and in humans and animals (ruminants). Representing "superparasitism", almost all of the 39 described virophages (except Zamilon) interact negatively with giant viruses by affecting their replication and morphogenesis and their "adaptive immunity". This causes them to become regulators and, at the same time, defenders of the host of giant viruses protozoa and algae, which are organisms that determine the homeostasis of the aquatic environment. They are classified in the family Lavidaviridae with two genus (Sputnikovirus, Mavirus). However, in 2023, a proposal was presented that they should form the class Maveriviricetes, with four orders and seven families. Their specific structure, including their microsatellite (SSR-Simple Sequence Repeats) and the CVV (cell-virus-virophage, or transpovirion) system described with them, as well as their function, makes them, together with the biological features of giant viruses, form the basis for discussing the existence of a fourth domain in addition to Bacteria, Archaea, and Eukaryota. The paper also presents the hypothetical possibility of using them as a vector for vaccine antigens.
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Affiliation(s)
| | - Sara Chrzanowska
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland
| | - Natalia Gurgacz
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland
| | - Michał Stosik
- Institute of Biological Science, Faculty of Biological Sciences, University of Zielona Góra, 65-417 Zielona Góra, Poland
| | - Wiesław Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University of Toruń, 87-100 Toruń, Poland
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Diversity of Surface Fibril Patterns in Mimivirus Isolates. J Virol 2023; 97:e0182422. [PMID: 36728417 PMCID: PMC9972986 DOI: 10.1128/jvi.01824-22] [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: 02/03/2023] Open
Abstract
Among the most intriguing structural features in the known virosphere are mimivirus surface fibrils, proteinaceous filaments approximately 150 nm long, covering the mimivirus capsid surface. Fibrils are important to promote particle adhesion to host cells, triggering phagocytosis and cell infection. However, although mimiviruses are one of the most abundant viral entities in a plethora of biomes worldwide, there has been no comparative analysis on fibril organization and abundance among distinct mimivirus isolates. Here, we describe the isolation and characterization of Megavirus caiporensis, a novel lineage C mimivirus with surface fibrils organized as "clumps." This intriguing feature led us to expand our analyses to other mimivirus isolates. By employing a combined approach including electron microscopy, image processing, genomic sequencing, and viral prospection, we obtained evidence of at least three main patterns of surface fibrils that can be found in mimiviruses: (i) isolates containing particles with abundant fibrils, distributed homogeneously on the capsid surface; (ii) isolates with particles almost fibrilless; and (iii) isolates with particles containing fibrils in abundance, but organized as clumps, as observed in Megavirus caiporensis. A total of 15 mimivirus isolates were analyzed by microscopy, and their DNA polymerase subunit B genes were sequenced for phylogenetic analysis. We observed a unique match between evolutionarily-related viruses and their fibril profiles. Biological assays suggested that patterns of fibrils can influence viral entry in host cells. Our data contribute to the knowledge of mimivirus fibril organization and abundance, as well as raising questions on the evolution of those intriguing structures. IMPORTANCE Mimivirus fibrils are intriguing structures that have drawn attention since their discovery. Although still under investigation, the function of fibrils may be related to host cell adhesion. In this work, we isolated and characterized a new mimivirus, called Megavirus caiporensis, and we showed that mimivirus isolates can exhibit at least three different patterns related to fibril organization and abundance. In our study, evolutionarily-related viruses presented similar fibril profiles, and such fibrils may affect how those viruses trigger phagocytosis in amoebas. These data shed light on aspects of mimivirus particle morphology, virus-host interactions, and their evolution.
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Nasrin T, Hoque M, Ali S. Microsatellite signature analysis of twenty-one virophage genomes of the family Lavidaviridae. Gene X 2022; 851:147037. [DOI: 10.1016/j.gene.2022.147037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/21/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
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Sakhaee F, Mosayebi Amroabadi J, Razi S, Vaziri F, Abdolrahimi F, Moghaddam S, Rahimi Jamnani F, Siadat SD, Fateh A. Detection of Mimivirus from respiratory samples in tuberculosis-suspected patients. Sci Rep 2022; 12:8676. [PMID: 35606506 PMCID: PMC9126102 DOI: 10.1038/s41598-022-12757-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
Acanthamoeba polyphaga mimivirus (APMV), a species of amoeba-infecting giant viruses, has recently emerged as human respiratory pathogens. This study aimed to evaluate the presence of Mimivirus in respiratory samples, collected from tuberculosis (TB)-suspected patients. The study was performed on 10,166 clinical respiratory samples from April 2013 to December 2017. Mimivirus was detected using a suicide nested-polymerase chain reaction (PCR) and real-time PCR methods. Of 10,166 TB-suspected patients, 4 (0.04%) were positive for Mimivirus, including Mimivirus-53, Mimivirus-186, Mimivirus-1291, and Mimivirus-1922. Three out of four patients, hospitalized in the intensive care unit (ICU), were mechanically ventilated. All patients had an underlying disease, and the virus was detected in both sputum and bronchoalveolar lavage samples. In conclusion, Mimivirus was isolated from TB-suspected patients in a comprehensive study. The present results, similar to previous reports, showed that Mimiviruses could be related to pneumonia. Further studies in different parts of the world are needed to additional investigate the clinical importance of Mimivirus infection.
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Fernandes AO, Barros GS, Batista MVA. Metatranscriptomics Analysis Reveals Diverse Viral RNA in Cutaneous Papillomatous Lesions of Cattle. Evol Bioinform Online 2022; 18:11769343221083960. [PMID: 35633934 PMCID: PMC9133864 DOI: 10.1177/11769343221083960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/09/2022] [Indexed: 11/17/2022] Open
Abstract
Bovine papillomavirus (BPV) is associated with bovine papillomatosis, a disease that forms benign warts in epithelial tissues, as well as malignant lesions. Previous studies have detected a co-infection between BPV and other viruses, making it likely that these co-infections could influence disease progression. Therefore, this study aimed to identify and annotate viral genes in cutaneous papillomatous lesions of cattle. Sequences were obtained from the GEO database, and an RNA-seq computational pipeline was used to analyze 3 libraries from bovine papillomatous lesions. In total, 25 viral families were identified, including Poxviridae, Retroviridae, and Herpesviridae. All libraries shared similarities in the viruses and genes found. The viral genes shared similarities with BPV genes, especially for functions as virion entry pathway, malignant progression by apoptosis suppression and immune system control. Therefore, this study presents relevant data extending the current knowledge regarding the viral microbiome in BPV lesions and how other viruses could affect this disease.
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Affiliation(s)
- Adriana O Fernandes
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | - Gerlane S Barros
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | - Marcus VA Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
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Dutta D, Ravichandiran V, Sukla S. Virophages: association with human diseases and their predicted role as virus killers. Pathog Dis 2021; 79:6380487. [PMID: 34601577 DOI: 10.1093/femspd/ftab049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
The fascinating discovery of the first giant virus, Acanthamoeba polyphaga mimivirus (APMV), belonging to the family Mimiviridae in 2008, and its associated virophage, Sputnik, have left the world of microbiology awestruck. To date, about 18 virophages have been isolated from different environmental sources. With their unique feature of resisting host cell infection and lysis by giant viruses, analogous to bacteriophage, they have been assigned under the family Lavidaviridae. Genome of T-27, icosahedral-shaped, non-enveloped virophages, consist of dsDNA encoding four proteins, namely, major capsid protein, minor capsid protein, ATPase and cysteine protease, which are essential in the formation and assembly of new virophage particles during replication. A few virophage genomes have been observed to contain additional sequences like PolB, ZnR and S3H. Another interesting characteristic of virophage is that Mimivirus lineage A is immune to infection by the Zamilon virophage through a phenomenon termed MIMIVIRE, resembling the CRISPR-Cas mechanism in bacteria. Based on the fact that giant viruses have been found in clinical samples of hospital-acquired pneumonia and rheumatoid arthritis patients, virophages have opened a novel era in the search for cures of various diseases. This article aims to study the prospective role of virophages in the future of human therapeutics.
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Affiliation(s)
- Debrupa Dutta
- National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, PIN-700054, West Bengal, India
| | - Velayutham Ravichandiran
- National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, PIN-700054, West Bengal, India
| | - Soumi Sukla
- National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, PIN-700054, West Bengal, India
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Sahmi-Bounsiar D, Rolland C, Aherfi S, Boudjemaa H, Levasseur A, La Scola B, Colson P. Marseilleviruses: An Update in 2021. Front Microbiol 2021; 12:648731. [PMID: 34149639 PMCID: PMC8208085 DOI: 10.3389/fmicb.2021.648731] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 04/12/2021] [Indexed: 01/19/2023] Open
Abstract
The family Marseilleviridae was the second family of giant viruses that was described in 2013, after the family Mimiviridae. Marseillevirus marseillevirus, isolated in 2007 by coculture on Acanthamoeba polyphaga, is the prototype member of this family. Afterward, the worldwide distribution of marseilleviruses was revealed through their isolation from samples of various types and sources. Thus, 62 were isolated from environmental water, one from soil, one from a dipteran, one from mussels, and two from asymptomatic humans, which led to the description of 67 marseillevirus isolates, including 21 by the IHU Méditerranée Infection in France. Recently, five marseillevirus genomes were assembled from deep sea sediment in Norway. Isolated marseilleviruses have ≈250 nm long icosahedral capsids and 348–404 kilobase long mosaic genomes that encode 386–545 predicted proteins. Comparative genomic analyses indicate that the family Marseilleviridae includes five lineages and possesses a pangenome composed of 3,082 clusters of genes. The detection of marseilleviruses in both symptomatic and asymptomatic humans in stool, blood, and lymph nodes, and an up-to-30-day persistence of marseillevirus in rats and mice, raise questions concerning their possible clinical significance that are still under investigation.
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Affiliation(s)
- Dehia Sahmi-Bounsiar
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
| | - Clara Rolland
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
| | - Sarah Aherfi
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
| | - Hadjer Boudjemaa
- IHU Méditerranée Infection, Marseille, France.,Department of Biology, Faculty of Natural Science and Life, Hassiba Benbouali University of Chlef, Chlef, Algeria
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France.,Institut de Recherche pour le Développement (IRD), Assistance Publique- Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, Marseille, France
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Yarzábal LA, Salazar LMB, Batista-García RA. Climate change, melting cryosphere and frozen pathogens: Should we worry…? ENVIRONMENTAL SUSTAINABILITY (SINGAPORE) 2021; 4:489-501. [PMID: 38624658 PMCID: PMC8164958 DOI: 10.1007/s42398-021-00184-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 05/12/2021] [Accepted: 05/15/2021] [Indexed: 11/21/2022]
Abstract
Permanently frozen environments (glaciers, permafrost) are considered as natural reservoirs of huge amounts of microorganisms, mostly dormant, including human pathogens. Due to global warming, which increases the rate of ice-melting, approximately 4 × 1021 of these microorganisms are released annually from their frozen confinement and enter natural ecosystems, in close proximity to human settlements. Some years ago, the hypothesis was put forward that this massive release of potentially-pathogenic microbes-many of which disappeared from the face of the Earth thousands and even millions of years ago-could give rise to epidemics. The recent anthrax outbreaks that occurred in Siberia, and the presence of bacterial and viral pathogens in glaciers worldwide, seem to confirm this hypothesis. In that context, the present review summarizes the currently available scientific evidence that allows us to imagine a near future in which epidemic outbreaks, similar to the abovementioned, could occur as a consequence of the resurrection and release of microbes from glaciers and permafrost. Supplementary Information The online version of this article (10.1007/s42398-021-00184-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luis Andrés Yarzábal
- Unidad de Salud y Bienestar, Universidad Católica de Cuenca, Av. Las Américas and Calle Humboldt, Cuenca, Ecuador
- Centro de Investigación, Innovación y Transferencia de Tecnología (CIITT), Universidad Católica de Cuenca, Campus Miracielos, Ricaurte, Ecuador
| | - Lenys M. Buela Salazar
- Unidad de Salud y Bienestar, Universidad Católica de Cuenca, Av. Las Américas and Calle Humboldt, Cuenca, Ecuador
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico
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Pires de Souza GA, Rolland C, Nafeh B, La Scola B, Colson P. Giant virus-related sequences in the 5300-year-old Ötzi mummy metagenome. Virus Genes 2021; 57:222-227. [PMID: 33566217 DOI: 10.1007/s11262-021-01823-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022]
Abstract
Giant viruses have brought new perspectives on the virosphere. They have been increasingly described in humans, including in several metagenomic studies. Here, we searched into the metagenome of the 5300-year-old Ötzi mummy for the presence of giant virus-related sequences using MG-Digger pipeline. We found 19 reads (0.00006% of the total read number) that best matched (mean ± standard deviation (range) for e-values of 5.0E-6 ± 1.4E-6 (6.0E-5-4.0E-10) and for amino acid identity of 69.9 ± 8.7% (46.4-84.9%) and most significantly with sequences from various giant viruses, including mostly mimiviruses. This expands current knowledge on the ubiquity and relationship with humans of giant viruses.
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Affiliation(s)
- Gabriel Augusto Pires de Souza
- Institut de Recherche Pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 boulevard Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Departamento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Clara Rolland
- Institut de Recherche Pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 boulevard Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Bariaa Nafeh
- Institut de Recherche Pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Bernard La Scola
- Institut de Recherche Pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 boulevard Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Colson
- Institut de Recherche Pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 boulevard Jean Moulin, 13005, Marseille, France. .,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
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Rasmussen TS, Jakobsen RR, Castro-Mejía JL, Kot W, Thomsen AR, Vogensen FK, Nielsen DS, Hansen AK. Inter-vendor variance of enteric eukaryotic DNA viruses in specific pathogen free C57BL/6N mice. Res Vet Sci 2021; 136:1-5. [PMID: 33548686 DOI: 10.1016/j.rvsc.2021.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/16/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023]
Abstract
The laboratory mouse strain C57BL/6 is widely used as an animal model for various applications. It is becoming increasingly clear that the bacterial enteric community highly influences the phenotype. Eukaryotic viruses represent a sparsely investigated member of the enteric microbiome that might also affect the phenotype. We here investigated the presence of enteric eukaryotic DNA viruses (EDVs) in specific pathogen-free (SPF) C57BL/6N mice purchased from three vendors upon arrival and after being fed a low-fat diet (LFD) or high-fat diet (HFD). We detected genetic fragments of EDVs belonging to the viral families of Herpes-, Mimi-, Baculo- and Phycodnaviridae represented by two genera; Chlorovirus and Prasinovirus. The EDVs were detected in the mice upon arrival and persisted for 13 weeks. However, these signals of EDVs were only detected at notable levels in mice fed LFD from 2 out of 3 vendors, which suggested that the enteric composition of these EDVs were affected by both vendor (p < 0.003) and different dietary regimes (p < 0.013). This highlights the need of additional studies assessing the potential function of these EDVs that may influence the mouse phenotype and the reproducibility of animal studies using this C57BL/6N substrain.
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Affiliation(s)
| | | | | | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Allan Randrup Thomsen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Finn Kvist Vogensen
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | | | - Axel Kornerup Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
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14
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Shrinking of repeating unit length in leucine-rich repeats from double-stranded DNA viruses. Arch Virol 2020; 166:43-64. [PMID: 33052487 DOI: 10.1007/s00705-020-04820-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
Leucine-rich repeats (LRRs) are present in over 563,000 proteins from viruses to eukaryotes. LRRs repeat in tandem and have been classified into fifteen classes in which the repeat unit lengths range from 20 to 29 residues. Most LRR proteins are involved in protein-protein or ligand interactions. The amount of genome sequence data from viruses is increasing rapidly, and although viral LRR proteins have been identified, a comprehensive sequence analysis has not yet been done, and their structures, functions, and evolution are still unknown. In the present study, we characterized viral LRRs by sequence analysis and identified over 600 LRR proteins from 89 virus species. Most of these proteins were from double-stranded DNA (dsDNA) viruses, including nucleocytoplasmic large dsDNA viruses (NCLDVs). We found that the repeating unit lengths of 11 types are one to five residues shorter than those of the seven known corresponding LRR classes. The repeating units of six types are 19 residues long and are thus the shortest among all LRRs. In addition, two of the LRR types are unique and have not been observed in bacteria, archae or eukaryotes. Conserved strongly hydrophobic residues such as Leu, Val or Ile in the consensus sequences are replaced by Cys with high frequency. Phylogenetic analysis indicated that horizontal gene transfer of some viral LRR genes had occurred between the virus and its host. We suggest that the shortening might contribute to the survival strategy of viruses. The present findings provide a new perspective on the origin and evolution of LRRs.
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15
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Chelkha N, Levasseur A, La Scola B, Colson P. Host-virus interactions and defense mechanisms for giant viruses. Ann N Y Acad Sci 2020; 1486:39-57. [PMID: 33090482 DOI: 10.1111/nyas.14469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/28/2020] [Accepted: 07/26/2020] [Indexed: 12/26/2022]
Abstract
Giant viruses, with virions larger than 200 nm and genomes larger than 340 kilobase pairs, modified the now outdated perception of the virosphere. With virions now reported reaching up to 1.5 μm in size and genomes of up to 2.5 Mb encoding components shared with cellular life forms, giant viruses exhibit a complexity similar to microbes, such as bacteria and archaea. Here, we review interactions of giant viruses with their hosts and defense strategies of giant viruses against their hosts and coinfecting microorganisms or virophages. We also searched by comparative genomics for homologies with proteins described or suspected to be involved in defense mechanisms. Our search reveals that natural immunity and apoptosis seem to be crucial components of the host defense against giant virus infection. Conversely, giant viruses possess methods of hijacking host functions to counteract cellular antiviral responses. In addition, giant viruses may encode other unique and complex pathways to manipulate the host machinery and eliminate other competing microorganisms. Notably, giant viruses have evolved defense mechanisms against their virophages and they might trigger defense systems against other viruses through sequence integration. We anticipate that comparative genomics may help identifying genes involved in defense strategies of both giant viruses and their hosts.
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Affiliation(s)
- Nisrine Chelkha
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
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16
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Sakhaee F, Vaziri F, Bahramali G, Siadat SD, Fateh A. Pulmonary Infection Related to Mimivirus in Patient with Primary Ciliary Dyskinesia. Emerg Infect Dis 2020; 26:2524-2526. [PMID: 32946733 PMCID: PMC7510730 DOI: 10.3201/eid2610.191613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Primary ciliary dyskinesia is a rare autosomal recessive disorder that causes oto-sino-pulmonary disease. We report a case of pulmonary infection related to mimivirus in a 10-year-old boy with primary ciliary dyskinesia that was identified using molecular techniques. Our findings indicate that the lineage C of mimivirus may cause pneumonia in humans.
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17
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Sakhaee F, Vaziri F, Bahramali G, Siadat SD, Fateh A. Pulmonary Infection Related to Mimivirus in Patient with Primary Ciliary Dyskinesia. Emerg Infect Dis 2020. [DOI: 10.3201/eid2608.191613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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18
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Behloul N, Baha S, Shi R, Meng J. Role of the GTNGTKR motif in the N-terminal receptor-binding domain of the SARS-CoV-2 spike protein. Virus Res 2020; 286:198058. [PMID: 32531235 PMCID: PMC7282740 DOI: 10.1016/j.virusres.2020.198058] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/18/2020] [Accepted: 06/07/2020] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2 S1-NTD presents different receptor binding motifs compared to the SARS-CoV. Functional motifs similar to the S1-NTD GTNGTKR loop were identified in other proteins. The GTNGTKR loop is very likely to allow the SARS-CoV-2 to bind other receptors. The GTNGTKR motif is very likely an evolutionary acquisition under functional constraints.
The 2019 novel coronavirus disease (COVID-19) that emerged in China has been declared as public health emergency of international concern by the World Health Organization and the causative pathogen was named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this report, we analyzed the structural characteristics of the N-terminal domain of the S1 subunit (S1-NTD) of the SARS-CoV-2 spike protein in comparison to the SARS-CoV in particular, and to other viruses presenting similar characteristic in general. Given the severity and the wide and rapid spread of the SARS-CoV-2 infection, it is very likely that the virus recognizes other receptors/co-receptors besides the ACE2. The NTD of the SARS-CoV-2 contains a receptor-binding motif different from that of SARS-CoV, with some insertions that could confer to the new coronavirus new receptor binding abilities. In particular, motifs similar to the insertion 72GTNGTKR78 have been found in structural proteins of other viruses; and these motifs were located in putative regions involved in recognizing protein and sugar receptors, suggesting therefore that similar binding abilities could be displayed by the SARS-CoV-2 S1-NTD. Moreover, concerning the origin of these NTD insertions, our findings point towards an evolutionary acquisition rather than the hypothesis of an engineered virus.
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MESH Headings
- Amino Acid Sequence
- Angiotensin-Converting Enzyme 2
- Animals
- Betacoronavirus/chemistry
- Betacoronavirus/genetics
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Chiroptera
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Evolution, Molecular
- Gene Expression
- Host-Pathogen Interactions/drug effects
- Host-Pathogen Interactions/genetics
- Humans
- Middle East Respiratory Syndrome Coronavirus/chemistry
- Middle East Respiratory Syndrome Coronavirus/genetics
- Middle East Respiratory Syndrome Coronavirus/metabolism
- Models, Molecular
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/genetics
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Severe acute respiratory syndrome-related coronavirus/chemistry
- Severe acute respiratory syndrome-related coronavirus/genetics
- Severe acute respiratory syndrome-related coronavirus/metabolism
- SARS-CoV-2
- Sequence Alignment
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Structural Homology, Protein
- Thermodynamics
- Virus Attachment
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Affiliation(s)
- Nouredine Behloul
- College of Basic Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Sarra Baha
- Department of Gastroenterology, Zhongda Hospital, Southeast University, Nanjing, 210009, Jiangsu Province, China
| | - Ruihua Shi
- Department of Gastroenterology, Zhongda Hospital, Southeast University, Nanjing, 210009, Jiangsu Province, China.
| | - Jihong Meng
- College of Basic Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.
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19
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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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20
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Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC. Diversity, evolution, and classification of virophages uncovered through global metagenomics. MICROBIOME 2019; 7:157. [PMID: 31823797 PMCID: PMC6905037 DOI: 10.1186/s40168-019-0768-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/11/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Virophages are small viruses with double-stranded DNA genomes that replicate along with giant viruses and co-infect eukaryotic cells. Due to the paucity of virophage reference genomes, a collective understanding of the global virophage diversity, distribution, and evolution is lacking. RESULTS Here we screened a public collection of over 14,000 metagenomes using the virophage-specific major capsid protein (MCP) as "bait." We identified 44,221 assembled virophage sequences, of which 328 represent high-quality (complete or near-complete) genomes from diverse habitats including the human gut, plant rhizosphere, and terrestrial subsurface. Comparative genomic analysis confirmed the presence of four core genes in a conserved block. We used these genes to establish a revised virophage classification including 27 clades with consistent genome length, gene content, and habitat distribution. Moreover, for eight high-quality virophage genomes, we computationally predicted putative eukaryotic virus hosts. CONCLUSION Overall, our approach has increased the number of known virophage genomes by 10-fold and revealed patterns of genome evolution and global virophage distribution. We anticipate that the expanded diversity presented here will provide the backbone for further virophage studies.
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Affiliation(s)
- David Paez-Espino
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
| | - Jinglie Zhou
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
| | - Simon Roux
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
| | - Stephen Nayfach
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
| | - Georgios A. Pavlopoulos
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
- BSRC “Alexander Fleming”, 34 Fleming Street, Vari, 16672 Athens, Greece
| | - Frederik Schulz
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
| | - Katherine D. McMahon
- Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, Madison, WI 53726 USA
| | - David Walsh
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6 Canada
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
| | - Natalia N. Ivanova
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
| | - Emiley A. Eloe-Fadrosh
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
| | - Susannah G. Tringe
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598 USA
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21
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Protozoal giant viruses: agents potentially infectious to humans and animals. Virus Genes 2019; 55:574-591. [PMID: 31290063 PMCID: PMC6746690 DOI: 10.1007/s11262-019-01684-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
The discovery of giant viruses has revolutionised the knowledge on viruses and transformed the idea of three domains of life. Here, we discuss the known protozoal giant viruses and their potential to infect also humans and animals.
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22
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Akashi M, Fukaya S, Uchiyama C, Aoki K, Takemura M. Visualization of giant virus particles and development of "VIRAMOS" for high school and university biology course. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:426-431. [PMID: 31021444 DOI: 10.1002/bmb.21249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/15/2019] [Accepted: 03/31/2019] [Indexed: 06/09/2023]
Abstract
Several educational trials on handling viruses and or virology have been reported. However, given their small size, direct visualization of these viruses under a microscope has been rarely performed. The so-called "giant viruses" are larger than other viruses with a particle size greater than 200-300 nm. This enables their direct visualization under a light microscope more easily than other viruses. In this study, we developed two new types of teaching material for learning about viruses and cellular organisms using mimivirus, one of the well-known giant viruses. One teaching material involves using glass slides with enclosed mimivirus particles, and another is a paper-based teaching material, named VIRAMOS (http://tlab-edusys.azurewebsites.net/content/viramos_en.pdf). Using these, students can investigate and learn about viruses and cellular organisms. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):426-431, 2019.
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Affiliation(s)
- Motohiro Akashi
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science (RIKADAI), Kagurazaka, Shinjuku, Tokyo, Japan
| | - Sho Fukaya
- Laboratory of Biology Education, Graduate School of Mathematics and Science Education, Tokyo University of Science (RIKADAI), Kagurazaka, Shinjuku, Tokyo, Japan
| | - Chieko Uchiyama
- Laboratory of Biology Education, Graduate School of Mathematics and Science Education, Tokyo University of Science (RIKADAI), Kagurazaka, Shinjuku, Tokyo, Japan
| | - Keita Aoki
- Laboratory of Biology Education, Graduate School of Mathematics and Science Education, Tokyo University of Science (RIKADAI), Kagurazaka, Shinjuku, Tokyo, Japan
| | - Masaharu Takemura
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science (RIKADAI), Kagurazaka, Shinjuku, Tokyo, Japan
- Laboratory of Biology Education, Graduate School of Mathematics and Science Education, Tokyo University of Science (RIKADAI), Kagurazaka, Shinjuku, Tokyo, Japan
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23
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Rolland C, Andreani J, Louazani AC, Aherfi S, Francis R, Rodrigues R, Silva LS, Sahmi D, Mougari S, Chelkha N, Bekliz M, Silva L, Assis F, Dornas F, Khalil JYB, Pagnier I, Desnues C, Levasseur A, Colson P, Abrahão J, La Scola B. Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere. Viruses 2019; 11:E312. [PMID: 30935049 PMCID: PMC6520786 DOI: 10.3390/v11040312] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022] Open
Abstract
The history of giant viruses began in 2003 with the identification of Acanthamoeba polyphaga mimivirus. Since then, giant viruses of amoeba enlightened an unknown part of the viral world, and every discovery and characterization of a new giant virus modifies our perception of the virosphere. This notably includes their exceptional virion sizes from 200 nm to 2 µm and their genomic complexity with length, number of genes, and functions such as translational components never seen before. Even more surprising, Mimivirus possesses a unique mobilome composed of virophages, transpovirons, and a defense system against virophages named Mimivirus virophage resistance element (MIMIVIRE). From the discovery and isolation of new giant viruses to their possible roles in humans, this review shows the active contribution of the University Hospital Institute (IHU) Mediterranee Infection to the growing knowledge of the giant viruses' field.
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Affiliation(s)
- Clara Rolland
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Julien Andreani
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Amina Cherif Louazani
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Sarah Aherfi
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Rania Francis
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Rodrigo Rodrigues
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- Laboratório de Vírus, Instituto de Ciêncas Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil.
| | - Ludmila Santos Silva
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Dehia Sahmi
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Said Mougari
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Nisrine Chelkha
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Meriem Bekliz
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Lorena Silva
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- Laboratório de Vírus, Instituto de Ciêncas Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil.
| | - Felipe Assis
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Fábio Dornas
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | | | - Isabelle Pagnier
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Christelle Desnues
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Anthony Levasseur
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Philippe Colson
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Jônatas Abrahão
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- Laboratório de Vírus, Instituto de Ciêncas Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil.
| | - Bernard La Scola
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
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24
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Chatterjee A, Sicheritz-Pontén T, Yadav R, Kondabagil K. Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India. Sci Rep 2019; 9:3690. [PMID: 30842490 PMCID: PMC6403294 DOI: 10.1038/s41598-019-40171-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/04/2019] [Indexed: 11/09/2022] Open
Abstract
We report the detection of genomic signatures of giant viruses (GVs) in the metagenomes of three environment samples from Mumbai, India, namely, a pre-filter of a household water purifier, a sludge sample from wastewater treatment plant (WWTP), and a drying bed sample of the same WWTP. The de novo assembled contigs of each sample yielded 700 to 2000 maximum unique matches with the GV genomic database. In all three samples, the maximum number of reads aligned to Pandoraviridae, followed by Phycodnaviridae, Mimiviridae, Iridoviridae, and other Megaviruses. We also isolated GVs from every environmental sample (n = 20) we tested using co-culture of the sample with Acanthomoeba castellanii. From this, four randomly selected GVs were subjected to the genomic characterization that showed remarkable cladistic homology with the three GV families viz., Mimivirirdae (Mimivirus Bombay [MVB]), Megaviruses (Powai lake megavirus [PLMV] and Bandra megavius [BAV]), and Marseilleviridae (Kurlavirus [KV]). All 4 isolates exhibited remarkable genomic identity with respective GV families. Functionally, the genomes were indistinguishable from other previously reported GVs, encoding nearly all COGs across extant family members. Further, the uncanny genomic homogeneity exhibited by individual GV families across distant geographies indicate their yet to be ascertained ecological significance.
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Affiliation(s)
- Anirvan Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Thomas Sicheritz-Pontén
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Rajesh Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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Ye Y, Zhao X, Lu Y, Long B, Zhang S. Varinostat Alters Gene Expression Profiles in Aortic Tissues from ApoE -/- Mice. HUM GENE THER CL DEV 2018; 29:214-225. [PMID: 30284929 DOI: 10.1089/humc.2018.141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Atherosclerosis (AS) is a complex, chronic inflammatory disease that is characterized by plaque buildup within arterial vessel walls. Preclinical trials have suggested that vorinostat, a pan-histone deacetylase inhibitor (HDACi), reduces vascular inflammation and AS, but the underlying protective mechanism has not been fully elucidated. The present study aimed to identify altered gene expression profiles in aortic tissues from ApoE-/- mice after vorinostat treatment. Male ApoE-/- mice fed a high-fat diet were treated with either vorinostat or vehicle, and the aortic plaque area was quantified 8 weeks after treatment. Aortic tissues were collected from both the vorinostat group (n = 3) and vehicle group (n = 3) for deep sequencing of the cDNA to construct sRNA libraries. Oral administration of vorinostat significantly reduced plaque size in the ApoE-/- mice (p < 0.05). In total, 1,550 differentially expressed mRNAs, 56 differentially expressed miRNAs, and 381 differentially expressed lncRNAs were identified in the vorinostat group compared to the vehicle group. Subsequently, a global lncRNA-miRNA-mRNA triple network was constructed based on the competitive endogenous RNA (ceRNA) theory. The hepatitis C signaling pathway was significantly enriched among the differentially expressed mRNAs from the ceRNA network, which suggests that vorinostat has anti-inflammatory properties. Importantly, the identified target pair of mmu-miR-3075-5p/lncRNA-A330023F24Rik/Ldlr may regulate drug response. Upregulation of low-density lipid receptor (Ldlr) and lncRNA-A330023F24Rik and downregulation of mmu-miR-3075-5p were further verified by quantitative real-time polymerase chain reaction. To conclude, vorinostat reduced AS in ApoE-/- mice. Differentially expressed mRNA, lncRNAs, and miRNAs, as well as their interactions and pathways, were identified, which partially explain vorinostat's anti-atherosclerotic effects.
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Affiliation(s)
- Yicong Ye
- 1 Department of Cardiology and Beijing Anzhen Hospital and Capital Medical University, Beijing, P.R. China.,2 Department of Department of Cardiology, Beijing Anzhen Hospital and Capital Medical University, Beijing, P.R. China
| | - Xiliang Zhao
- 1 Department of Cardiology and Beijing Anzhen Hospital and Capital Medical University, Beijing, P.R. China
| | - Yiyun Lu
- 1 Department of Cardiology and Beijing Anzhen Hospital and Capital Medical University, Beijing, P.R. China
| | - Bo Long
- 3 Department of Central Laboratory, Chinese Academy of Medical College and Peking Union Medical College Hospital, Peking Union Medical College Hospital, Beijing, P.R. China
| | - Shuyang Zhang
- 1 Department of Cardiology and Beijing Anzhen Hospital and Capital Medical University, Beijing, P.R. China
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Abat C, Rolain JM, Colson P. Investigations by the Institut Hospitalo-Universitaire Méditerranée Infection of food and food-borne infections in the Mediterranean Basin and in sub-Saharan Africa. New Microbes New Infect 2018; 26:S37-S42. [PMID: 30402242 PMCID: PMC6205566 DOI: 10.1016/j.nmni.2018.08.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 07/02/2018] [Accepted: 08/22/2018] [Indexed: 12/25/2022] Open
Abstract
Food-borne infections are major causes of public health concern in developing and developed countries. During the past decade, the Institut Hospitalo-Universitaire Méditerranée Infection has conducted or been involved in multiple investigations that aimed at identifying the sources and strains responsible for food-borne diseases and therefore at improving the understanding, diagnosis, prevention and control of these infections. Investigations were conducted in the Mediterranean area and in sub-Saharan Africa on more than 15 food-borne agents, 17 food products and 14 antibiotic resistance-associated genes. Multiple sources, including unexpected ones, and pathogens, including emerging ones, were involved. Travelling in developing countries and zoonoses are major contributors to food-borne infections, while food-borne transmission of resistance-associated genes is increasingly reported. However, risk factors and pathogens associated with food-borne infections likely remain untapped and must be more extensively investigated, monitored and regularly reassessed. Diagnostic tests based on new technologies and real-time surveillance tools based on microbiology laboratory data are promising approaches to detect known food-borne infections and decipher new ones. Studies of the microbiota and its relationships with dietary patterns are also worth being conducted.
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Colson P, Ominami Y, Hisada A, La Scola B, Raoult D. Giant mimiviruses escape many canonical criteria of the virus definition. Clin Microbiol Infect 2018; 25:147-154. [PMID: 30267933 DOI: 10.1016/j.cmi.2018.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/05/2018] [Accepted: 09/10/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND The discovery of mimivirus in 2003 prompted the quest for other giant viruses of amoebae. Mimiviruses and their relatives were found to differ considerably from other viruses. Their study led to major advances in virology and evolutionary biology. AIMS We summarized the widening gap between mimiviruses and other viruses. SOURCES We collected data from articles retrieved from PubMed using as keywords 'giant virus', 'mimivirus' and 'virophage', as well as quoted references from these articles. CONTENT Data accumulated during the last 15 years on mimiviruses and other giant viruses highlight that there is a quantum leap between these infectious agents, the complexity of which is similar to that of intracellular microorganisms, and classical viruses. Notably, in addition to their giant structures and genomes, giant viruses have abundant gene repertoires with genes unique in the virosphere, including a tremendous set of translation components. The viruses contain hundreds of proteins and many transcripts. They share a core of central and ancient proteins but their genome sequences display a substantial level of mosaicism. Finally, mimiviruses have a specific mobilome, including virophages that can integrate into their genomes, and against which they can defend themselves through integration of short fragments of the DNA of these invaders. IMPLICATIONS Mimiviruses and subsequently discovered giant viruses have changed the virus paradigm and contradict many virus definition criteria delineated for classical viruses. The major cellular hallmark that is still lacking in giant viruses is the ribosome, including both ribosomal protein and RNA encoding genes, which makes them bona fide microbes without ribosomes.
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Affiliation(s)
- P Colson
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Y Ominami
- Hitachi High-Technologies Corporation, Science & Medical Systems Business Group, Minato-ku, Tokyo, Japan
| | - A Hisada
- Hitachi Ltd, Research & Development Group, Saitama, Japan
| | - B La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - D Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France.
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28
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Zara V, Ferramosca A, Günnewig K, Kreimendahl S, Schwichtenberg J, Sträter D, Çakar M, Emmrich K, Guidato P, Palmieri F, Rassow J. Mimivirus-Encoded Nucleotide Translocator VMC1 Targets the Mitochondrial Inner Membrane. J Mol Biol 2018; 430:5233-5245. [PMID: 30261167 DOI: 10.1016/j.jmb.2018.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/18/2018] [Accepted: 09/18/2018] [Indexed: 01/08/2023]
Abstract
Mimivirus (Acanthamoeba polyphaga mimivirus) was the first giant DNA virus identified in an amoeba species. Its genome contains at least 979 genes. One of these, L276, encodes a nucleotide translocator with similarities to mitochondrial metabolite carriers, provisionally named viral mitochondrial carrier 1 (VMC1). In this study, we investigated the intracellular distribution of VMC1 upon expression in HeLa cells and in the yeast Saccharomyces cerevisiae. We found that VMC1 is specifically targeted to mitochondria and to the inner mitochondrial membrane. Newly synthesized VMC1 binds to the mitochondrial outer-membrane protein Tom70 and translocates through the import channel formed by the β-barrel protein Tom40. Derivatization of the four cysteine residues inside Tom40 by N-ethylmaleimide caused a delay in translocation but not a complete occlusion. Cell viability was not reduced by VMC1. Neither the mitochondrial membrane potential nor the intracellular production of reactive oxygen species was affected. Similar to endogenous metabolite carriers, mimivirus-encoded VMC1 appears to act as a specific translocator in the mitochondrial inner membrane. Due to its permeability for deoxyribonucleotides, VMC1 confers to the mitochondria an opportunity to contribute nucleotides for the replication of the large DNA genome of the virus.
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Affiliation(s)
- Vincenzo Zara
- Department of Environmental and Biological Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Alessandra Ferramosca
- Department of Environmental and Biological Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Kathrin Günnewig
- Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Sebastian Kreimendahl
- Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Jan Schwichtenberg
- Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Dina Sträter
- Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Mahmut Çakar
- Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Kerstin Emmrich
- Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Patrick Guidato
- Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Joachim Rassow
- Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780 Bochum, Germany.
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Healthcare-Associated Viral Infections: Considerations for Nosocomial Transmission and Infection Control. HEALTHCARE-ASSOCIATED INFECTIONS IN CHILDREN 2018. [PMCID: PMC7121921 DOI: 10.1007/978-3-319-98122-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nosocomial and healthcare-associated viral infections are major contributors to patient morbidity and mortality, prolonged hospitalization, and increased healthcare costs in all pediatric age groups. Healthcare workers are also at risk of acquiring nosocomial viral infections, affecting their own health, as well as facilitating spread of the infection to other patients, their family, and the community. Healthcare-associated viral infections may occur in a variety of healthcare settings, including clinics, emergency centers, urgent care centers, procedure suites, operating rooms, hospital wards, nurseries, and intensive care units. In addition, non-patient care areas, such as the cafeteria, waiting areas, and playrooms may also be a source of viral infections that can spread in the healthcare setting. These infections may be device-related or transmitted via blood products or organ donation and respiratory droplets, through food including human milk, person to person, or via air ducts, fomites, and surfaces. They most commonly involve the respiratory and gastrointestinal tracts; however, all organ systems may potentially be involved. Both DNA and RNA viruses, either common or exotic, may contribute to healthcare-associated viral infections. Advances in molecular viral diagnostics have enabled rapid detection and routine surveillance for viral infections and now allow early identification of viruses. Prompt identification allows timely containment measures to minimize transmission to other patients or healthcare workers and avoids hospital, community, and global outbreaks.
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30
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Elbehery AHA, Feichtmayer J, Singh D, Griebler C, Deng L. The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation. Front Microbiol 2018; 9:1110. [PMID: 29896176 PMCID: PMC5987705 DOI: 10.3389/fmicb.2018.01110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/09/2018] [Indexed: 12/19/2022] Open
Abstract
Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually untapped resource of diversity, functional and physiological information. Here we present the human virome protein cluster database as an effort to improve functional annotation and characterization of human viromes. The database was built out of hundreds of virome datasets from six different body sites. We also show the utility of this database through its use for the characterization of three bronchoalveolar lavage (BAL) viromes from one healthy control in addition to one moderate and one severe chronic obstructive pulmonary disease (COPD) patients. The use of the database allowed for a better functional annotation, which were otherwise poorly characterized when limited to annotation using sequences from full-length viral genomes. In addition, our BAL samples gave a first insight into viral communities of COPD patients and confirm a state of dysbiosis for viruses that increases with disease progression. Moreover, they shed light on the potential role of phages in the horizontal gene transfer of bacterial virulence factors, a phenomenon that highlights a possible contribution of phages to etiopathology.
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Affiliation(s)
- Ali H A Elbehery
- Institute of Virology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Judith Feichtmayer
- Institute of Groundwater Ecology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Dave Singh
- EvA Consortium, Manchester, United Kingdom.,Medicines Evaluation Unit, University Hospital of South Manchester Foundation Trust, University of Manchester, Manchester, United Kingdom
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
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Lagier JC, Drancourt M, Charrel R, Bittar F, La Scola B, Ranque S, Raoult D. Many More Microbes in Humans: Enlarging the Microbiome Repertoire. Clin Infect Dis 2018; 65:S20-S29. [PMID: 28859350 DOI: 10.1093/cid/cix404] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The proportion of cultured microorganisms is dramatically lower than those predicted to be involved in colonization, acute, or chronic infections. We report our laboratory's contribution to promoting culture methods. As a result of using culturomics in our clinical microbiology laboratories (including amoeba co-culture and shell-vial culture) and through the use of matrix-assisted laser desorption/ionization-time-of-flight and the 16S rRNA gene for identification, we cultured 329 new bacterial species. This is also the first time that 327 of species have been isolated from humans, increasing the known human bacterial repertoire by 29%. We isolated 4 archaeal species for the first time from human, including 2 new species. Of the 100 isolates of giant viruses, we demonstrated the human pathogenicity of Mimivirus in pneumonia and Marseillevirus in diverse clinical situations. From sand flies, we isolated most of the known Phlebovirus strains that potentially cause human infections. Increasing the repertoire of human-associated microorganisms through culture will allow us to test pathogenicity models with viable microorganisms.
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Affiliation(s)
| | | | - Rémi Charrel
- UMR Emergence des Pathologies Virales, IRD 190, Inserm 1207, EHESP, France Fondation, IHU Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM) Public Hospitals of Marseille
| | | | | | - Stéphane Ranque
- Université Montpellier 1, IRBA, IP-TPT, Aix Marseille Université.,Parasitologie and Mycologie, IHU Méditerranée Infection, Hôpital de la Timone, AP-HM, Marseille, France
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32
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Abrahão J, Silva L, Oliveira D, Almeida G. Lack of evidence of mimivirus replication in human PBMCs. Microbes Infect 2018; 20:281-283. [PMID: 29604428 DOI: 10.1016/j.micinf.2018.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/20/2018] [Accepted: 03/17/2018] [Indexed: 10/17/2022]
Abstract
The Acanthamoeba polyphaga mimivirus (APMV) was first isolated during a pneumonia outbreak in Bradford, England, and since its discovery many research groups devoted efforts to understand whether this virus could be associated to human diseases, in particular clinical signs and symptoms of pneumonia. In 2013, we observed cytopathic effect in amoebas (rounding and lysis) inoculated with APMV inoculated PBMCs (peripheral blood mononuclear cell) extracts, and at that point we interpreted those results as mimivirus replication in human PBMCs. Based on these results we decided to further investigate APMV replication in human PBMCs, by transmission electron microscopy (TEM) and qPCR. No viral factory was observed in APMV inoculated PBMCs, at any analyzed time and M.O.I.s (multiplicity of infection), by checking 550 cells per condition tested. We also measured the variation of viral DNA by qPCR targeting helicase gene during the course of the TEM experiment in PBMCs, but the DNA levels stayed the same as the first time-point post infection. In summary, our newest qPCR and TEM results do not support previous statements (including ours) that mimivirus is able to replicate in humans PBMCs.
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Affiliation(s)
- Jônatas Abrahão
- Universidade Federal de Minas Gerais, Laboratório de Vírus, Belo Horizonte, Brazil.
| | - Lorena Silva
- Universidade Federal de Minas Gerais, Laboratório de Vírus, Belo Horizonte, Brazil.
| | - Danilo Oliveira
- Universidade Federal dos Vales do Jequitinhonha e do Mucuri, Diamantina, Brazil.
| | - Gabriel Almeida
- Department of Biological and Environmental Science, University of Jyvaskyla, FI-40014 Jyvaskyla, Finland.
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Aherfi S, Nappez C, Lepidi H, Bedotto M, Barassi L, Jardot P, Colson P, La Scola B, Raoult D, Bregeon F. Experimental Inoculation in Rats and Mice by the Giant Marseillevirus Leads to Long-Term Detection of Virus. Front Microbiol 2018; 9:463. [PMID: 29619012 PMCID: PMC5871663 DOI: 10.3389/fmicb.2018.00463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
The presence of the giant virus of amoeba Marseillevirus has been identified at many different sites on the human body, including in the bloodstream of asymptomatic subjects, in the lymph nodes of a child with adenitis, in one adult with Hodgkin's disease, and in the pharynx of an adult. A high seroprevalence of the Marseillevirus has been recorded in the general population. Whether Marseillevirus can disseminate and persist within a mammal after entry remains unproven. We aimed to assess the ability of the virus to disseminate and persist into healthy organisms, especially in the lymphoid organs. Parenteral inoculations were performed by intraperitoneal injection (in rats and mice) or intravenous injection (in rats). Airway inoculation was performed by aerosolization (in mice). Dissemination and persistence were assessed by using PCR and amebal co-culture. Serologies were performed by immunofluorescent assay. Pathological examination was conducted after standard and immunohistochemistry staining. After intraperitoneal inoculation in mice and rats, Marseillevirus was detected in the bloodstream during the first 24 h. Persistence was noted until the end of the experiment, i.e., at 14 days in rats. After intravenous inoculation in rats, the virus was first detected in the blood until 48 h and then in deep organs with infectious virus detected until 14 and 21 days in the liver and the spleen, respectively. Its DNA was detected for up to 30 days in the liver and the spleen. After aerosolization in mice, infectious Marseillevirus was present in the lungs and nasal associated lymphoid tissue until 30 days post inoculation but less frequently and at a lower viral load in the lung than in the nasal associated lymphoid tissue. No other site of dissemination was found after aerosol exposure. Despite no evidence of disease being observed, the 30-day long persistence of Marseillevirus in rats and mice, regardless of the route of inoculation, supports the hypothesis of an infective potential of the virus in certain conditions. Its constant and long-term detection in nasal associated lymphoid tissue in mice after an aerosol exposure suggests the involvement of naso-pharyngeal associated lymphoid tissues in protecting the host against environmental Marseillevirus.
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Affiliation(s)
- Sarah Aherfi
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Claude Nappez
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Hubert Lepidi
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France.,Laboratoire d'Anatomopathologie, Centre Hospitalo Universitaire Timone, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Marielle Bedotto
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Lina Barassi
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Priscilla Jardot
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Philippe Colson
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Bernard La Scola
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Didier Raoult
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Fabienne Bregeon
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France.,Service des Explorations Fonctionnelles Respiratoires Centre Hospitalo Universitaire Nord, Pôle Cardio-Vasculaire et thoracique, Assistance Publique des Hôpitaux de Marseille, Marseille, France
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Cedratvirus getuliensis replication cycle: an in-depth morphological analysis. Sci Rep 2018; 8:4000. [PMID: 29507337 PMCID: PMC5838162 DOI: 10.1038/s41598-018-22398-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/22/2018] [Indexed: 01/30/2023] Open
Abstract
The giant viruses are the largest and most complex viruses in the virosphere. In the last decade, new members have constantly been added to this group. Here, we provide an in-depth descriptive analysis of the replication cycle of Cedratvirus getuliensis, one of the largest viruses known to date. We tracked the virion entry, the early steps of virus factory and particles morphogenesis, and during this phase, we observed a complex and unique sequential organization of immature particle elements, including horseshoe and rectangular compartments, revealed by transverse and longitudinal sections, respectively, until the formation of the final ovoid-shaped striped virion. The genome and virion proteins are incorporated through a longitudinal opening in the immature virion, followed by the incorporation of the second cork and thickening of the capsid well. Moreover, many cell modifications occur during viral infection, including intense membrane trafficking important to viral morphogenesis and release, as evidenced by treatment using brefeldin A. Finally, we observed that Cedratvirus getuliensis particles are released after cellular lysis, although we obtained microscopic evidence that some particles are released by exocytosis. The present study provides new information on the unexplored steps in the life cycle of cedratviruses.
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Aherfi S, Colson P, Raoult D. Marseillevirus in the Pharynx of a Patient with Neurologic Disorders. Emerg Infect Dis 2018; 22:2008-2010. [PMID: 27767918 PMCID: PMC5088024 DOI: 10.3201/eid2211.160189] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Andrade ACDSP, Arantes TS, Rodrigues RAL, Machado TB, Dornas FP, Landell MF, Furst C, Borges LGA, Dutra LAL, Almeida G, Trindade GDS, Bergier I, Abrahão W, Borges IA, Cortines JR, de Oliveira DB, Kroon EG, Abrahão JS. Ubiquitous giants: a plethora of giant viruses found in Brazil and Antarctica. Virol J 2018; 15:22. [PMID: 29368617 PMCID: PMC5784613 DOI: 10.1186/s12985-018-0930-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/12/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Since the discovery of giant viruses infecting amoebae in 2003, many dogmas of virology have been revised and the search for these viruses has been intensified. Over the last few years, several new groups of these viruses have been discovered in various types of samples and environments.In this work, we describe the isolation of 68 giant viruses of amoeba obtained from environmental samples from Brazil and Antarctica. METHODS Isolated viruses were identified by hemacolor staining, PCR assays and electron microscopy (scanning and/or transmission). RESULTS A total of 64 viruses belonging to the Mimiviridae family were isolated (26 from lineage A, 13 from lineage B, 2 from lineage C and 23 from unidentified lineages) from different types of samples, including marine water from Antarctica, thus being the first mimiviruses isolated in this extreme environment to date. Furthermore, a marseillevirus was isolated from sewage samples along with two pandoraviruses and a cedratvirus (the third to be isolated in the world so far). CONCLUSIONS Considering the different type of samples, we found a higher number of viral groups in sewage samples. Our results reinforce the importance of prospective studies in different environmental samples, therefore improving our comprehension about the circulation anddiversity of these viruses in nature.
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Affiliation(s)
- Ana Cláudia Dos S P Andrade
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thalita S Arantes
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo A L Rodrigues
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Talita B Machado
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fábio P Dornas
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Melissa F Landell
- Laboratório de Diversidade Molecular, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Brazil
| | - Cinthia Furst
- Departamento de Patologia, Universidade Federal do Espírito Santo, Maruípe, Brazil
| | - Luiz G A Borges
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Instituto do Petróleo e dos Recursos Naturais (IPR), Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lara A L Dutra
- Department of Biological and Environmental Sciences, University of Jyvaskyla, Jyvaskyla, Finland
| | - Gabriel Almeida
- Department of Biological and Environmental Sciences, University of Jyvaskyla, Jyvaskyla, Finland
| | - Giliane de S Trindade
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Iara A Borges
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Juliana R Cortines
- Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Danilo B de Oliveira
- Faculdade de Medicina, Universidade Federal do dos Vales do Jequitinhonha e Mucuri, Diamantina, Brazil
| | - Erna G Kroon
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jônatas S Abrahão
- Laboratorio de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Almeida GMDF, Silva LCF, Colson P, Abrahao JS. Mimiviruses and the Human Interferon System: Viral Evasion of Classical Antiviral Activities, But Inhibition By a Novel Interferon-β Regulated Immunomodulatory Pathway. J Interferon Cytokine Res 2018; 37:1-8. [PMID: 28079476 DOI: 10.1089/jir.2016.0097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In this review we discuss the role of mimiviruses as potential human pathogens focusing on clinical and evolutionary evidence. We also propose a novel antiviral immunomodulatory pathway controlled by interferon-β (IFN-β) and mediated by immune-responsive gene 1 (IRG1) and itaconic acid, its product. Acanthamoeba polyphaga Mimivirus (APMV) was isolated from amoebae in a hospital while investigating a pneumonia outbreak. Mimivirus ubiquity and role as protist pathogens are well understood, and its putative status as a human pathogen has been gaining strength as more evidence is being found. The study of APMV and human cells interaction revealed that the virus is able to evade the IFN system by inhibiting the regulation of interferon-stimulated genes, suggesting that the virus and humans have had host-pathogen interactions. It also has shown that the virus is capable of growing on IFN-α2, but not on IFN-β-treated cells, hinting at an exclusive IFN-β antiviral pathway. Our hypothesis based on preliminary data and published articles is that IFN-β preferentially upregulates IRG1 in human macrophagic cells, which in turn produces itaconic acid. This metabolite links metabolism to antiviral activity by inactivating the virus, in a novel immunomodulatory pathway relevant for APMV infections and probably to other infectious diseases as well.
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Affiliation(s)
| | - Lorena C Ferreira Silva
- 2 Laboratorio de Virus, Departamento de Microbiologia, Universidade Federal de Minas Gerais , Belo Horizonte, Brazil
| | - Philippe Colson
- 3 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix-Marseille Universite Faculté de Médecine , Marseille, France
| | - Jonatas Santos Abrahao
- 2 Laboratorio de Virus, Departamento de Microbiologia, Universidade Federal de Minas Gerais , Belo Horizonte, Brazil .,3 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix-Marseille Universite Faculté de Médecine , Marseille, France
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Diesend J, Kruse J, Hagedorn M, Hammann C. Amoebae, Giant Viruses, and Virophages Make Up a Complex, Multilayered Threesome. Front Cell Infect Microbiol 2018; 7:527. [PMID: 29376032 PMCID: PMC5768912 DOI: 10.3389/fcimb.2017.00527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/13/2017] [Indexed: 01/28/2023] Open
Abstract
Viral infection had not been observed for amoebae, until the Acanthamoeba polyphaga mimivirus (APMV) was discovered in 2003. APMV belongs to the nucleocytoplasmatic large DNA virus (NCLDV) family and infects not only A. polyphaga, but also other professional phagocytes. Here, we review the Megavirales to give an overview of the current members of the Mimi- and Marseilleviridae families and their structural features during amoebal infection. We summarize the different steps of their infection cycle in A. polyphaga and Acanthamoeba castellani. Furthermore, we dive into the emerging field of virophages, which parasitize upon viral factories of the Megavirales family. The discovery of virophages in 2008 and research in recent years revealed an increasingly complex network of interactions between cell, giant virus, and virophage. Virophages seem to be highly abundant in the environment and occupy the same niches as the Mimiviridae and their hosts. Establishment of metagenomic and co-culture approaches rapidly increased the number of detected virophages over the recent years. Genetic interaction of cell and virophage might constitute a potent defense machinery against giant viruses and seems to be important for survival of the infected cell during mimivirus infections. Nonetheless, the molecular events during co-infection and the interactions of cell, giant virus, and virophage have not been elucidated, yet. However, the genetic interactions of these three, suggest an intricate, multilayered network during amoebal (co-)infections. Understanding these interactions could elucidate molecular events essential for proper viral factory activity and could implicate new ways of treating viruses that form viral factories.
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Affiliation(s)
- Jan Diesend
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Janis Kruse
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Monica Hagedorn
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
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Moal V, Kodangasse W, Aherfi S, Berland Y, Raoult D, Colson P, La Scola B. Mimivirus in the urine of a kidney-transplant recipient. Clin Microbiol Infect 2018; 24:561-563. [PMID: 29309939 DOI: 10.1016/j.cmi.2017.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/20/2017] [Accepted: 12/23/2017] [Indexed: 10/18/2022]
Affiliation(s)
- V Moal
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France; AP-HM, Hôpital Conception, Centre de Néphrologie et Transplantation Rénale, Marseille, France
| | - W Kodangasse
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - S Aherfi
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Y Berland
- AP-HM, Hôpital Conception, Centre de Néphrologie et Transplantation Rénale, Marseille, France; Aix Marseille Université, Marseille, France
| | - D Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - P Colson
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - B La Scola
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
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Assis FL, Franco-Luiz APM, Dos Santos RN, Campos FS, Dornas FP, Borato PVM, Franco AC, Abrahao JS, Colson P, Scola BL. Genome Characterization of the First Mimiviruses of Lineage C Isolated in Brazil. Front Microbiol 2017; 8:2562. [PMID: 29312242 PMCID: PMC5743647 DOI: 10.3389/fmicb.2017.02562] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/11/2017] [Indexed: 01/01/2023] Open
Abstract
The family Mimiviridae, comprised by giant DNA viruses, has been increasingly studied since the isolation of the Acanthamoeba polyphaga mimivirus (APMV), in 2003. In this work, we describe the genome analysis of two new mimiviruses, each isolated from a distinct Brazilian environment. Furthermore, for the first time, we are reporting the genomic characterization of mimiviruses of group C in Brazil (Br-mimiC), where a predominance of mimiviruses from group A has been previously reported. The genomes of the Br-mimiC isolates Mimivirus gilmour (MVGM) and Mimivirus golden (MVGD) are composed of double-stranded DNA molecules of ∼1.2 Mb, each encoding more than 1,100 open reading frames. Genome functional annotations highlighted the presence of mimivirus group C hallmark genes, such as the set of seven aminoacyl-tRNA synthetases. However, the set of tRNA encoded by the Br-mimiC was distinct from those of other group C mimiviruses. Differences could also be observed in a genome synteny analysis, which demonstrated the presence of inversions and loci translocations at both extremities of Br-mimiC genomes. Both phylogenetic and phyletic analyses corroborate previous results, undoubtedly grouping the new Brazilian isolates into mimivirus group C. Finally, an updated pan-genome analysis of genus Mimivirus was performed including all new genomes available until the present moment. This last analysis showed a slight increase in the number of clusters of orthologous groups of proteins among mimiviruses of group A, with a larger increase after addition of sequences from mimiviruses of groups B and C, as well as a plateau tendency after the inclusion of the last four mimiviruses of group C, including the Br-mimiC isolates. Future prospective studies will help us to understand the genetic diversity among mimiviruses.
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Affiliation(s)
- Felipe L Assis
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana P M Franco-Luiz
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Raíssa N Dos Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fabrício S Campos
- College of Veterinary Medicine and Agronomy, University of Brasília, Brasília, Brazil
| | - Fábio P Dornas
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paulo V M Borato
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana C Franco
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jônatas S Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Philippe Colson
- CNRS 7278, IRD 198, INSERM 1095, UM63, IHU - Méditerranée Infection, AP-HM, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université, Marseille, France
| | - Bernard La Scola
- CNRS 7278, IRD 198, INSERM 1095, UM63, IHU - Méditerranée Infection, AP-HM, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université, Marseille, France
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41
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Colson P, Aherfi S, La Scola B. Evidence of giant viruses of amoebae in the human gut. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.humic.2017.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Sobhy H. A comparative review of viral entry and attachment during large and giant dsDNA virus infections. Arch Virol 2017; 162:3567-3585. [PMID: 28866775 PMCID: PMC5671522 DOI: 10.1007/s00705-017-3497-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 07/13/2017] [Indexed: 12/19/2022]
Abstract
Viruses enter host cells via several mechanisms, including endocytosis, macropinocytosis, and phagocytosis. They can also fuse at the plasma membrane and can spread within the host via cell-to-cell fusion or syncytia. The mechanism used by a given viral strain depends on its external topology and proteome and the type of cell being entered. This comparative review discusses the cellular attachment receptors and entry pathways of dsDNA viruses belonging to the families Adenoviridae, Baculoviridae, Herpesviridae and nucleocytoplasmic large DNA viruses (NCLDVs) belonging to the families Ascoviridae, Asfarviridae, Iridoviridae, Phycodnaviridae, and Poxviridae, and giant viruses belonging to the families Mimiviridae and Marseilleviridae as well as the proposed families Pandoraviridae and Pithoviridae. Although these viruses have several common features (e.g., topology, replication and protein sequence similarities) they utilize different entry pathways to infect wide-range of hosts, including humans, other mammals, invertebrates, fish, protozoa and algae. Similarities and differences between the entry methods used by these virus families are highlighted, with particular emphasis on viral topology and proteins that mediate viral attachment and entry. Cell types that are frequently used to study viral entry are also reviewed, along with other factors that affect virus-host cell interactions.
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Affiliation(s)
- Haitham Sobhy
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden.
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Arroyo Mühr LS, Bzhalava Z, Hortlund M, Lagheden C, Nordqvist Kleppe S, Bzhalava D, Hultin E, Dillner J. Viruses in cancers among the immunosuppressed. Int J Cancer 2017; 141:2498-2504. [DOI: 10.1002/ijc.31017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 07/17/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Laila Sara Arroyo Mühr
- Karolinska Institutet; Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital; Huddinge Stockholm 141 86 Sweden
| | - Zurab Bzhalava
- Karolinska Institutet; Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital; Huddinge Stockholm 141 86 Sweden
| | - Maria Hortlund
- Karolinska Institutet; Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital; Huddinge Stockholm 141 86 Sweden
| | - Camilla Lagheden
- Karolinska Institutet; Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital; Huddinge Stockholm 141 86 Sweden
| | - Sara Nordqvist Kleppe
- Karolinska Institutet; Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital; Huddinge Stockholm 141 86 Sweden
| | - Davit Bzhalava
- Karolinska Institutet; Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital; Huddinge Stockholm 141 86 Sweden
| | - Emilie Hultin
- Karolinska Institutet; Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital; Huddinge Stockholm 141 86 Sweden
| | - Joakim Dillner
- Karolinska Institutet; Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital; Huddinge Stockholm 141 86 Sweden
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Colson P, La Scola B, Raoult D. Giant Viruses of Amoebae: A Journey Through Innovative Research and Paradigm Changes. Annu Rev Virol 2017; 4:61-85. [PMID: 28759330 DOI: 10.1146/annurev-virology-101416-041816] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Giant viruses of amoebae were discovered serendipitously in 2003; they are visible via optical microscopy, making them bona fide microbes. Their lifestyle, structure, and genomes break the mold of classical viruses. Giant viruses of amoebae are complex microorganisms. Their genomes harbor between 444 and 2,544 genes, including many that are unique to viruses, and encode translation components; their virions contain >100 proteins as well as mRNAs. Mimiviruses have a specific mobilome, including virophages, provirophages, and transpovirons, and can resist virophages through a system known as MIMIVIRE (mimivirus virophage resistance element). Giant viruses of amoebae bring upheaval to the definition of viruses and tend to separate the current virosphere into two categories: very simple viruses and viruses with complexity similar to that of other microbes. This new paradigm is propitious for enhanced detection and characterization of giant viruses of amoebae, and a particular focus on their role in humans is warranted.
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Affiliation(s)
- Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France;
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France;
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France;
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Dornas FP, Boratto PVM, Costa GB, Silva LCF, Kroon EG, La Scola B, Trindade G, Abrahão JS. Detection of mimivirus genome and neutralizing antibodies in humans from Brazil. Arch Virol 2017; 162:3205-3207. [DOI: 10.1007/s00705-017-3455-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/15/2017] [Indexed: 11/27/2022]
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Abbas AA, Diamond J, Chehoud C, Chang B, Kotzin J, Young J, Imai I, Haas A, Cantu E, Lederer D, Meyer K, Milewski R, Olthoff K, Shaked A, Christie J, Bushman F, Collman R. The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction. Am J Transplant 2017; 17:1313-1324. [PMID: 27731934 PMCID: PMC5389935 DOI: 10.1111/ajt.14076] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 01/25/2023]
Abstract
Primary graft dysfunction (PGD) is a principal cause of early morbidity and mortality after lung transplantation, but its pathogenic mechanisms are not fully clarified. To date, studies using standard clinical assays have not linked microbial factors to PGD. We previously used comprehensive metagenomic methods to characterize viruses in lung allografts >1 mo after transplant and found that levels of Anellovirus, mainly torque teno viruses (TTVs), were significantly higher than in nontransplanted healthy controls. We used quantitative polymerase chain reaction to analyze TTV and shotgun metagenomics to characterize full viral communities in acellular bronchoalveolar lavage from donor organs and postreperfusion allografts in PGD and non-PGD lung transplant recipient pairs. Unexpectedly, TTV DNA levels were elevated 100-fold in donor lungs compared with healthy adults (p = 0.0026). Although absolute TTV levels did not differ by PGD status, PGD cases showed a smaller increase in TTV levels from before to after transplant than did control recipients (p = 0.041). Metagenomic sequencing revealed mainly TTV and bacteriophages of respiratory tract bacteria, but no viral taxa distinguished PGD cases from controls. These findings suggest that conditions associated with brain death promote TTV replication and that greater immune activation or tissue injury associated with PGD may restrict TTV abundance in the lung.
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Affiliation(s)
- A. A. Abbas
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.M. Diamond
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - C. Chehoud
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - B. Chang
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.J. Kotzin
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.C. Young
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - I. Imai
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - A.R. Haas
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - E. Cantu
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - D.J. Lederer
- Departments of Medicine and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY
| | - K. Meyer
- School of Medicine and Public Health, University of Wisconsin, Madison, WI
| | - R.K. Milewski
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - K.M. Olthoff
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - A. Shaked
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.D. Christie
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - F.D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Corresponding authors: Frederic Bushman: , Ronald Collman:
| | - R.G. Collman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Corresponding authors: Frederic Bushman: , Ronald Collman:
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Colson P, La Scola B, Levasseur A, Caetano-Anollés G, Raoult D. Mimivirus: leading the way in the discovery of giant viruses of amoebae. Nat Rev Microbiol 2017; 15:243-254. [PMID: 28239153 PMCID: PMC7096837 DOI: 10.1038/nrmicro.2016.197] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acanthamoeba polyphaga mimivirus (APMV) and subsequently discovered giant viruses of amoebae challenge the previous definition of viruses and their classification. The replication cycle, structure, genomic make-up and plasticity of giant viruses differ from those of traditional viruses. They extend the definition of viruses into a broader range of biological entities, some of which are very simple and others of which have a complexity that is comparable to that of other microorganisms. Giant viruses of amoebae have virus particles as large as some microorganisms that are visible by light microscopy and that have a stunning level of complexity. Their genomes are mosaics and contain large repertoires of genes, some of which are hallmarks of cellular organisms, although the majority of which have unknown functions. Mimiviruses are associated with a specific mobilome and are parasitized by viruses that they can defend against. Several hypotheses on the ancient origin and evolutionary relationship between cellular organisms and giant viruses of amoebae have been proposed, and these topics continue to be debated. The detection of giant viruses of amoebae in humans and the study of their potential pathogenicity are emerging fields.
The discovery of the giant amoebal virus mimivirus, in 2003, opened up a new area of virology. Extended studies, including those of mimiviruses, have since revealed that these viruses have genetic, proteomic and structural features that are more complex than those of conventional viruses. The accidental discovery of the giant virus of amoeba — Acanthamoeba polyphaga mimivirus (APMV; more commonly known as mimivirus) — in 2003 changed the field of virology. Viruses were previously defined by their submicroscopic size, which probably prevented the search for giant viruses, which are visible by light microscopy. Extended studies of giant viruses of amoebae revealed that they have genetic, proteomic and structural complexities that were not thought to exist among viruses and that are comparable to those of bacteria, archaea and small eukaryotes. The giant virus particles contain mRNA and more than 100 proteins, they have gene repertoires that are broader than those of other viruses and, notably, some encode translation components. The infection cycles of giant viruses of amoebae involve virus entry by amoebal phagocytosis and replication in viral factories. In addition, mimiviruses are infected by virophages, defend against them through the mimivirus virophage resistance element (MIMIVIRE) system and have a unique mobilome. Overall, giant viruses of amoebae, including mimiviruses, marseilleviruses, pandoraviruses, pithoviruses, faustoviruses and molliviruses, challenge the definition and classification of viruses, and have increasingly been detected in humans.
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Affiliation(s)
- Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix-Marseille University, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille, France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix-Marseille University, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille, France
| | - Anthony Levasseur
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix-Marseille University, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille, France
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, 332 National Soybean Research Center, 1101 West Peabody Drive, Urbana, Illinois 61801, USA
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix-Marseille University, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille, France
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Abrahão JS, Araújo R, Colson P, La Scola B. The analysis of translation-related gene set boosts debates around origin and evolution of mimiviruses. PLoS Genet 2017; 13:e1006532. [PMID: 28207761 PMCID: PMC5313130 DOI: 10.1371/journal.pgen.1006532] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The giant mimiviruses challenged the well-established concept of viruses, blurring the roots of the tree of life, mainly due to their genetic content. Along with other nucleo-cytoplasmic large DNA viruses, they compose a new proposed order-named Megavirales-whose origin and evolution generate heated debate in the scientific community. The presence of an arsenal of genes not widespread in the virosphere related to important steps of the translational process, including transfer RNAs, aminoacyl-tRNA synthetases, and translation factors for peptide synthesis, constitutes an important element of this debate. In this review, we highlight the main findings to date about the translational machinery of the mimiviruses and compare their distribution along the distinct members of the family Mimiviridae. Furthermore, we discuss how the presence and/or absence of the translation-related genes among mimiviruses raises important insights to boost the debate on their origin and evolutionary history.
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Affiliation(s)
- Jônatas Santos Abrahão
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille, France.,Instituto de Ciências Biológicas, Departamento de Microbiologia, Laboratório de Vírus, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Araújo
- Instituto de Ciências Biológicas, Departamento de Microbiologia, Laboratório de Vírus, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille, France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille, France
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Bajrai LH, de Assis FL, Azhar EI, Jardot P, Robert C, Abrahão J, Raoult D, La Scola B. Saudi Moumouvirus, the First Group B Mimivirus Isolated from Asia. Front Microbiol 2016; 7:2029. [PMID: 28066355 PMCID: PMC5167723 DOI: 10.3389/fmicb.2016.02029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/02/2016] [Indexed: 12/19/2022] Open
Abstract
The number of novel giant viruses identified and characterized from the recently proposed order Megavirales has increased in recent years and new questions have been raised regarding viral diversity and evolution. Here, we describe the isolation and characterization of Saudi moumouvirus (SDMV), a new giant virus belonging to Mimivirus lineage B, isolated from a sewage sample taken from the King Abdulaziz University hospital in Jeddah, Saudi Arabia. SDMV presented 500 nm icosahedral particles with a 1,046,087 bp genome, which is larger than moumouvirus-like genomes which have been described in the past. The SDMV genome was predicted to encode 868 ORFs, ranging in size from 54 to 2,914 amino acids, with a mean size of 349 aa. Furthermore, this genome was predicted to encode 40 new genes (ORFans) without similarity with other sequences (ORFan L850 transcript was detected by qPCR in infected amoeba), in addition to 42 hypothetical proteins (pseudo-ORFs) with less than 100 aa, which matched other sequences in the NCBI nr database. Phylogenetic analysis showed that SDMV clustered together with mimiviruses from lineage B, including moumouvirus-like strains. It is, therefore, the third Mimivirus to be isolated in Asia and the first of group B.
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Affiliation(s)
- Leena H Bajrai
- Department of Biochemistry, Faculty of Science, King Abdulaziz UniversityJeddah, Saudi Arabia; Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille UniversitéMarseille, France
| | - Felipe L de Assis
- Laboratório de Vírus, Belo Horizonte, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Minas Gerais, Brazil
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, and Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah Saudi Arabia
| | - Priscilla Jardot
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille Université Marseille, France
| | - Catherine Robert
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille Université Marseille, France
| | - Jônatas Abrahão
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille UniversitéMarseille, France; Laboratório de Vírus, Belo Horizonte, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas GeraisMinas Gerais, Brazil
| | - Didier Raoult
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille Université Marseille, France
| | - Bernard La Scola
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille Université Marseille, France
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