Viruses of Protozoa

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: closed (14 November 2016) | Viewed by 70570

Special Issue Editor

1 Aix-Marseille Univ., Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Marseille, France
2 Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique – Hôpitaux de Marseille, Marseille, France
Interests: giant viruses, viruses of protozoa, virophages, intracellular bacteria, fastidious bacteria, taxonomy, emerging pathogens, necrotizing enterocolitis

Special Issue Information

Dear Colleagues,

Viruses have been identified in a wide variety of organisms, from simple prokaryotes to multicellular animals and higher plants . After observation of virus-like particles in protozoa using electron microscopy, viruses in protozoa were definitely identified in the eighties. First observations were done in Plasmodium, Naegleria, Leishmania, Entamoeba, then Trichomonas and Babesia. Most of these viruses are usually small with particles less than 70 nm and genome above 7 kbp.
Larger viruses of protozoa later described were Phycodnaviridae, a family of large double stranded DNA viruses (100-560 kb) that infect marine or freshwater eukaryotic algae. This family belongs to a super-group of large viruses known as nucleocytoplasmic large DNA viruses (NCLDVs) incorporating also Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Mimiviridae and the proposed family “Marseilleviridae”. The family Mimiviridae includes the largest known viruses, with genomes in excess of one megabase, whereas the genome size in the other NCLDV families varies from 100 to 400 kilobase pairs.
During the last past years, new virus families encompassing several members, namely pandoraviruses, Pithovirus sibericum, Mollivirus sibericum and faustoviruses were described to be associated with several protozoa, mostly free living amoeba. These viruses are characterized by large particles and genomes, up to 1 µm et 2.5 mbp for Pandoravirus salinus. They were even demonstrated to be infected by small viruses named virophages and to defend against these virophages using a system resembling that of CRISPR/Cas in prokaryotes. The members of this new order, proposed as Megavirales, are increasingly demonstrated to stand in the tree of life aside Bacteria, Archaea and Eukarya, and the megavirus ancestor is suspected to be as ancient as cellular ancestors.

This special issue contains both reviews and updates on research relating to viruses of protozoa, including description of new isolates of viruses, analyzis of their biology, genomics and metagenomics, proteomics and interaction with their protozoan host.

Bernard La Scola
Guest Editor

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Keywords

  • virus of protozoa
  • megavirales
  • virophages
  • giant viruses
  • NCLDV

Published Papers (8 papers)

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Research

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1324 KiB  
Article
MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales
by Sourabh Jain, Arup Panda, Philippe Colson, Didier Raoult and Pierre Pontarotti
Viruses 2017, 9(4), 72; https://doi.org/10.3390/v9040072 - 07 Apr 2017
Cited by 2 | Viewed by 5501
Abstract
With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the [...] Read more.
With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the major drawback in gene acquisition studies is the focus on few MV families or putative families with large variation in their genetic structure. Thus, here we have tried to develop a methodology by which we can detect horizontal gene transfers (HGTs), taking into consideration orthologous groups of distantly related Megavirale families. Here, we report an automated workflow MimiLook, prepared as a Perl command line program, that deduces orthologous groups (OGs) from ORFomes of Megavirales and constructs phylogenetic trees by performing alignment generation, alignment editing and protein-protein BLAST (BLASTP) searching across the National Center for Biotechnology Information (NCBI) non-redundant (nr) protein sequence database. Finally, this tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detection of HGTs, along with retrieval of information about those OGs that are monophyletic with organisms from cellular domains of life. By implementing MimiLook, we noticed that nine percent of Megavirale gene families (i.e., OGs) have been acquired by HGT, 80% OGs were Megaviralespecific and eight percent were found to be sharing common ancestry with members of cellular domains (Eukaryote, Bacteria, Archaea, Phages or other viruses) and three percent were ambivalent. The results are briefly discussed to emphasize methodology. Also, MimiLook is relevant for detecting evolutionary scenarios in other targeted phyla with user defined modifications. It can be accessed at following link 10.6084/m9.figshare.4653622. Full article
(This article belongs to the Special Issue Viruses of Protozoa)
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61439 KiB  
Article
Microscopic Characterization of the Brazilian Giant Samba Virus
by Jason R. Schrad, Eric J. Young, Jônatas S. Abrahão, Juliana R. Cortines and Kristin N. Parent
Viruses 2017, 9(2), 30; https://doi.org/10.3390/v9020030 - 14 Feb 2017
Cited by 14 | Viewed by 12166
Abstract
Prior to the discovery of the mimivirus in 2003, viruses were thought to be physically small and genetically simple. Mimivirus, with its ~750-nm particle size and its ~1.2-Mbp genome, shattered these notions and changed what it meant to be a virus. Since this [...] Read more.
Prior to the discovery of the mimivirus in 2003, viruses were thought to be physically small and genetically simple. Mimivirus, with its ~750-nm particle size and its ~1.2-Mbp genome, shattered these notions and changed what it meant to be a virus. Since this discovery, the isolation and characterization of giant viruses has exploded. One of the more recently discovered giant viruses, Samba virus, is a Mimivirus that was isolated from the Rio Negro in the Brazilian Amazon. Initial characterization of Samba has revealed some structural information, although the preparation techniques used are prone to the generation of structural artifacts. To generate more native-like structural information for Samba, we analyzed the virus through cryo-electron microscopy, cryo-electron tomography, scanning electron microscopy, and fluorescence microscopy. These microscopy techniques demonstrated that Samba particles have a capsid diameter of ~527 nm and a fiber length of ~155 nm, making Samba the largest Mimivirus yet characterized. We also compared Samba to a fiberless mimivirus variant. Samba particles, unlike those of mimivirus, do not appear to be rigid, and quasi-icosahedral, although the two viruses share many common features, including a multi-layered capsid and an asymmetric nucleocapsid, which may be common amongst the Mimiviruses. Full article
(This article belongs to the Special Issue Viruses of Protozoa)
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603 KiB  
Article
A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window
by Lucie Gallot-Lavallée and Guillaume Blanc
Viruses 2017, 9(1), 17; https://doi.org/10.3390/v9010017 - 20 Jan 2017
Cited by 40 | Viewed by 7015
Abstract
The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of [...] Read more.
The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases. A total of 66 eukaryotic genomic or transcriptomic datasets—many of which are from algae and aquatic protists—contained at least one of the five most consistently conserved NCLDV core genes. Phylogenetic study of the eukaryotic NCLDV-like sequences identified putative new members of already recognized viral families, as well as members of as yet unknown viral clades. Genomic evidence suggested that most of these sequences resulted from viral DNA integrations rather than contaminating viruses. Furthermore, the nature of the inserted viral genes helped predicting original functional capacities of the donor viruses. These insights confirm that genomic insertions of NCLDV DNA are common in eukaryotes and can be exploited to delineate the contours of NCLDV biodiversity. Full article
(This article belongs to the Special Issue Viruses of Protozoa)
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4572 KiB  
Article
Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses
by Julien Andreani, Sarah Aherfi, Jacques Yaacoub Bou Khalil, Fabrizio Di Pinto, Idir Bitam, Didier Raoult, Philippe Colson and Bernard La Scola
Viruses 2016, 8(11), 300; https://doi.org/10.3390/v8110300 - 03 Nov 2016
Cited by 73 | Viewed by 9079
Abstract
Most viruses are known for the ability to cause symptomatic diseases in humans and other animals. The discovery of Acanthamoeba polyphaga mimivirus and other giant amoebal viruses revealed a considerable and previously unknown area of uncharacterized viral particles. Giant viruses have been isolated [...] Read more.
Most viruses are known for the ability to cause symptomatic diseases in humans and other animals. The discovery of Acanthamoeba polyphaga mimivirus and other giant amoebal viruses revealed a considerable and previously unknown area of uncharacterized viral particles. Giant viruses have been isolated from various environmental samples collected from very distant geographic places, revealing a ubiquitous distribution. Their morphological and genomic features are fundamental elements for classifying them. Herein, we report the isolation and draft genome of Cedratvirus, a new amoebal giant virus isolated in Acanthamoeba castellanii, from an Algerian environmental sample. The viral particles are ovoid-shaped, resembling Pithovirus sibericum, but differing notably in the presence of two corks at each extremity of the virion. The draft genome of Cedratvirus—589,068 base pairs in length—is a close relative of the two previously described pithoviruses, sharing 104 and 113 genes with P. sibericum and Pithovirus massiliensis genomes, respectively. Interestingly, analysis of these viruses’ core genome reveals that only 21% of Cedratvirus genes are involved in best reciprocal hits with the two pithoviruses. Phylogeny reconstructions and comparative genomics indicate that Cedratvirus is most closely related to pithoviruses, and questions their membership in an enlarged putative Pithoviridae family. Full article
(This article belongs to the Special Issue Viruses of Protozoa)
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3842 KiB  
Article
Kaumoebavirus, a New Virus That Clusters with Faustoviruses and Asfarviridae
by Leena H. Bajrai, Samia Benamar, Esam I. Azhar, Catherine Robert, Anthony Levasseur, Didier Raoult and Bernard La Scola
Viruses 2016, 8(11), 278; https://doi.org/10.3390/v8110278 - 28 Oct 2016
Cited by 62 | Viewed by 7685
Abstract
In this study, we report the isolation of a new giant virus found in sewage water from the southern area of Jeddah (Saudi Arabia), with morphological and genomic resemblance to Faustoviruses. This new giant virus, named Kaumoebavirus, was obtained from co-culture with Vermamoeba [...] Read more.
In this study, we report the isolation of a new giant virus found in sewage water from the southern area of Jeddah (Saudi Arabia), with morphological and genomic resemblance to Faustoviruses. This new giant virus, named Kaumoebavirus, was obtained from co-culture with Vermamoeba vermiformis, an amoeboid protozoa considered to be of special interest to human health and the environment. This new virus has ~250 nm icosahedral capsids and a 350,731 bp DNA genome length. The genome of Kaumoebavirus has a coding density of 86%, corresponding to 465 genes. Most of these genes (59%) are closely related to genes from members of the proposed order Megavirales, and the best matches to its proteins with other members of the Megavirales are Faustoviruses (43%) and Asfarviruses (23%). Unsurprisingly, phylogenetic reconstruction places Kaumoebavirus as a distant relative of Faustoviruses and Asfarviruses. Full article
(This article belongs to the Special Issue Viruses of Protozoa)
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Review

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1067 KiB  
Review
Free-Living Amoebae as Hosts for and Vectors of Intracellular Microorganisms with Public Health Significance
by Carsten Balczun and Patrick L. Scheid
Viruses 2017, 9(4), 65; https://doi.org/10.3390/v9040065 - 01 Apr 2017
Cited by 96 | Viewed by 8964
Abstract
Free-living amoebae (FLA) are parasites within both humans and animals causing a wide range of symptoms and act as hosts of, and vehicles for phylogenetically diverse microorganisms, called endocytobionts. The interaction of the FLA with sympatric microorganisms leads to an exceptional diversity within [...] Read more.
Free-living amoebae (FLA) are parasites within both humans and animals causing a wide range of symptoms and act as hosts of, and vehicles for phylogenetically diverse microorganisms, called endocytobionts. The interaction of the FLA with sympatric microorganisms leads to an exceptional diversity within FLA. Some of these bacteria, viruses, and even eukaryotes, can live and replicate intracellularly within the FLA. This relationship provides protection to the microorganisms from external interventions and a dispersal mechanism across various habitats. Among those intracellularly-replicating or -residing organisms there are obligate and facultative pathogenic microorganisms affecting the health of humans or animals and are therefore of interest to Public Health Authorities. Mimiviruses, Pandoraviruses, and Pithoviruses are examples for interesting viral endocytobionts within FLA. Future research is expected to reveal further endocytobionts within free-living amoebae and other protozoa through co-cultivation studies, genomic, transcriptomic, and proteomic analyses. Full article
(This article belongs to the Special Issue Viruses of Protozoa)
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2160 KiB  
Review
Promoter Motifs in NCLDVs: An Evolutionary Perspective
by Graziele Pereira Oliveira, Ana Cláudia dos Santos Pereira Andrade, Rodrigo Araújo Lima Rodrigues, Thalita Souza Arantes, Paulo Victor Miranda Boratto, Ludmila Karen dos Santos Silva, Fábio Pio Dornas, Giliane De Souza Trindade, Betânia Paiva Drumond, Bernard La Scola, Erna Geessien Kroon and Jônatas Santos Abrahão
Viruses 2017, 9(1), 16; https://doi.org/10.3390/v9010016 - 20 Jan 2017
Cited by 18 | Viewed by 9101
Abstract
For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding [...] Read more.
For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. Full article
(This article belongs to the Special Issue Viruses of Protozoa)
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1383 KiB  
Review
The Expanding Family of Virophages
by Meriem Bekliz, Philippe Colson and Bernard La Scola
Viruses 2016, 8(11), 317; https://doi.org/10.3390/v8110317 - 23 Nov 2016
Cited by 37 | Viewed by 9105
Abstract
Virophages replicate with giant viruses in the same eukaryotic cells. They are a major component of the specific mobilome of mimiviruses. Since their discovery in 2008, five other representatives have been isolated, 18 new genomes have been described, two of which being nearly [...] Read more.
Virophages replicate with giant viruses in the same eukaryotic cells. They are a major component of the specific mobilome of mimiviruses. Since their discovery in 2008, five other representatives have been isolated, 18 new genomes have been described, two of which being nearly completely sequenced, and they have been classified in a new viral family, Lavidaviridae. Virophages are small viruses with approximately 35–74 nm large icosahedral capsids and 17–29 kbp large double-stranded DNA genomes with 16–34 genes, among which a very small set is shared with giant viruses. Virophages have been isolated or detected in various locations and in a broad range of habitats worldwide, including the deep ocean and inland. Humans, therefore, could be commonly exposed to virophages, although currently limited evidence exists of their presence in humans based on serology and metagenomics. The distribution of virophages, the consequences of their infection and the interactions with their giant viral hosts within eukaryotic cells deserve further research. Full article
(This article belongs to the Special Issue Viruses of Protozoa)
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