Real-Time PCR Systems Targeting Giant Viruses of Amoebae and Their Virophages

Ngounga, Tatsiana; Pagnier, Isabelle; Reteno, Dorine-Gaelle Ikanga; Raoult, Didier; Scola, Bernard La; Colson, Philippe

doi:10.1159/000354563

Cited by 25 publications

(20 citation statements)

References 52 publications

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“…Protozoal lysis associated with virus infection was detected by cytometer analysis with an arbitrarily designated threshold of 50% lysis. Detection of mimivirus and marseillevirus DNAs was performed by PCR as previously described (17).…”

Section: Flow Cytometric Analyses (I) Detection Of Amoeba Lysis By Fmentioning

confidence: 99%

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

Reteno

Benamar

Khalil

et al. 2015

J Virol

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Giant viruses are protist-associated viruses belonging to the proposed order Megavirales; almost all have been isolated from Acanthamoeba spp. Their isolation in humans suggests that they are part of the human virome. Using a high-throughput strategy to isolate new giant viruses from their original protozoan hosts, we obtained eight isolates of a new giant viral lineage from Vermamoeba vermiformis, the most common free-living protist found in human environments. This new lineage was proposed to be the faustovirus lineage. The prototype member, faustovirus E12, forms icosahedral virions of Ϸ200 nm that are devoid of fibrils and that encapsidate a 466-kbp genome encoding 451 predicted proteins. Of these, 164 are found in the virion. Phylogenetic analysis of the core viral genes showed that faustovirus is distantly related to the mammalian pathogen African swine fever virus, but it encodes Ϸ3 times more mosaic gene complements. About two-thirds of these genes do not show significant similarity to genes encoding any known proteins. These findings show that expanding the panel of protists to discover new giant viruses is a fruitful strategy. IMPORTANCEBy using Vermamoeba, a protist living in humans and their environment, we isolated eight strains of a new giant virus that we named faustovirus. The genomes of these strains were sequenced, and their sequences showed that faustoviruses are related to but different from the vertebrate pathogen African swine fever virus (ASFV), which belongs to the family Asfarviridae. Moreover, the faustovirus gene repertoire is Ϸ3 times larger than that of ASFV and comprises approximately two-thirds ORFans (open reading frames [ORFs] with no detectable homology to other ORFs in a database). G iant viruses were first described in 2003, with the discovery of Acanthamoeba polyphaga mimivirus (1, 2). They are protistassociated viruses that belong to a major monophyletic group of double-stranded DNA (dsDNA) viruses known as nucleocytoplasmic large DNA viruses (NCLDVs), and they have been classified under the proposed order Megavirales (3). Since the first description of Acanthamoeba polyphaga mimivirus, giant viruses have been isolated from other phagocytic protists, primarily Acanthamoeba spp. (4-6). Because these giant viruses are resistant to killing by phagocytic protists, we hypothesized that they may also reproduce in macrophages and might therefore infect humans. This proposition was validated experimentally by the isolation of mimivirus from atypical pneumonia patients and by the detection of marseilleviruses in blood donors and in human lymph nodes (7-9). Moreover, we and others identified sequences associated with giant viruses in metagenomes generated from human tissues, suggesting that giant viruses are a component of the human virome (10). Because the investigation of a virome typically starts with a filtration procedure that eliminates giant viruses (11), we developed a new culture approach that does not prevent the detection of these viruses.In the present study, we de...

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Section: Flow Cytometric Analyses (I) Detection Of Amoeba Lysis By Fmentioning

confidence: 99%

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

Reteno

Benamar

Khalil

et al. 2015

J Virol

Self Cite

177

233

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“…Nevertheless, it is worth noticing that only three PCR systems were used in these studies and they only targeted the Mimivirus genome obtained in 2004 [23]. The family Mimiviridae has expanded since 2004 and genetic diversity has been shown to be substantial between mimiviruses [66,67], and, therefore, these PCR assays should have had limited or no efficiency to detect other Mimivirus DNA than that of the first Mimivirus strain [68]. …”

Section: Evidence Of Human Infection or Colonization With A Giant Virusmentioning

confidence: 99%

Giant Viruses of Amoebae as Potential Human Pathogens

2013

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Giant viruses infecting phagocytic protists are composed of mimiviruses, the record holders of particle and genome size amongst viruses, and marseilleviruses. Since the discovery in 2003 at our laboratory of the first of these giant viruses, the Mimivirus, a growing body of data has revealed that they are common inhabitants of our biosphere. Moreover, from the outset, the story of Mimivirus has been linked to that of patients exhibiting pneumonia and it was shown that patients developed antibodies to this amoebal pathogen. Since then, there have been several proven cases of human infection or colonization with giant viruses of amoebae, which are known to host several bacteria that are human pathogens. Mimiviruses and marseilleviruses represent a major challenge in human pathology, as virological procedures implemented to date have not used appropriate media to allow their culture, and molecular techniques have used filtration steps that likely prevented their detection. Nevertheless, there is an increasing body of evidence that mimiviruses might cause pneumonia and that humans carry marseilleviruses, and re-analyses of metagenomic databases have provided evidence that these giant viruses can be common in human samples. The proportion of human infections related to these giant mimiviruses and marseilleviruses and the precise short- and long-term consequences of these infections have been scarcely investigated so far and should be the subject of future works.

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“…DNA sequences were deposited in the Genbank (MG981284-7). Quantification of Mimivirus and Marseillevirus partial viral genome copies in the soil samples was performed as previously described by Ngounga et al [18].…”

Section: Introductionmentioning

confidence: 99%

Isolation and Quantification of Mimivirus-Like and Marseillevirus-Like Viruses from Soil Samples in An Aboriginal (Orang asli) Village in Peninsular Malaysia

et al. 2018

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Background: The giant amoebal viruses of Mimivirus and Marseillevirus are large DNA viruses and have been documented in water, soil, and sewage samples. The trend of discovering these giant amoebal viruses has been increasing throughout Asia with Japan, India, and Saudi Arabia being the latest countries to document the presence of these viruses. To date, there have been no reports of large amoebal viruses being isolated in South East Asia. Objective: In this study, we aim to discover these viruses from soil samples in an aboriginal village (Serendah village) in Peninsular Malaysia. Method and Results: We successfully detected and isolated both Mimivirus-like and Marseillevirus-like viruses using Acanthamoeba castellanii. Phylogeny analysis identified them as Mimivirus and Marseillevirus, respectively. Conclusion: The ubiquitous nature of both Mimivirus and Marseillevirus is further confirmed in our study as they are detected in higher quantity in soil that is near to water vicinities in an aboriginal village in Peninsular Malaysia. However, this study is limited by our inability to investigate the impact of Mimivirus and Marseillevirus on the aboriginal villagers. More studies on the potential impact of these viruses on human health, especially on the aborigines, are warranted.

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Real-Time PCR Systems Targeting Giant Viruses of Amoebae and Their Virophages

Cited by 25 publications

References 52 publications

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

Giant Viruses of Amoebae as Potential Human Pathogens

Isolation and Quantification of Mimivirus-Like and Marseillevirus-Like Viruses from Soil Samples in An Aboriginal <b><i>(</i></b>Orang asli<b><i>)</i></b> Village in Peninsular Malaysia

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