Pan-Genome Analysis of Brazilian Lineage A Amoebal Mimiviruses

Assis, Felipe Lopes de; Bajrai, Leena Hussein; Abrahão, Jônatas Santos; Kroon, Erna Geessien; Dornas, Fábio P.; Andrade, Kétyllen Reis; Boratto, Paulo Victor de Miranda; Pilotto, Mariana Rangel; Robert, Caroline; Benamar, Samia; Scola, Bernard La; Colson, Philippe

doi:10.3390/v7072782

Cited by 26 publications

(25 citation statements)

References 41 publications

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“…Since the first reported mimivirus isolation ( La Scola et al, 2003 ), many giant viruses have been detected and isolated from diverse environments and even in humans ( La Scola et al, 2003 , 2008 ; Arslan et al, 2011 ; Saadi et al, 2013a , b ; Campos et al, 2014 ; Dornas et al, 2014a ; Scheid et al, 2014 ; Andrade et al, 2015 ; Assis et al, 2015 ; Reteno et al, 2015 ). Isolation and detection have occurred at different rates in the different samples studied, with low positive detection and isolation in bronchoalveolar lavages and feces ( Saadi et al, 2013a , b ) and more strongly positive results in soil, water, and sewage ( Pagnier et al, 2013 ; Campos et al, 2014 ; Dornas et al, 2014a , b ; Assis et al, 2015 ; Reteno et al, 2015 ). The environmental samples chosen herein were previously described as sources for isolation of numerous giant viruses ( Gaze et al, 2011 ; Pagnier et al, 2013 ; Philippe et al, 2013 ; Assis et al, 2015 ; Reteno et al, 2015 ) and represent a good set of samples to compare different amoeba in their ability to isolate giant viruses.…”

Section: Discussionmentioning

confidence: 99%

“…As they have been isolated in a limited number of protozoa used to support co-culture, the natural host is usually unknown for most of them ( Colson et al, 2012 ). Members of the two recently created families Mimiviridae and Marseilleviridae have been detected and isolated from highly diverse environments including human samples ( La Scola et al, 2003 , 2008 ; Boyer et al, 2009 ; Arslan et al, 2011 ; Boughalmi et al, 2013a , b , c ; Ngounga et al, 2013 ; Saadi et al, 2013a , b ; Campos et al, 2014 ; Dornas et al, 2014a ; Scheid et al, 2014 ; Andrade et al, 2015 ; Assis et al, 2015 ; Reteno et al, 2015 ), and to date, considering protist hosts, these viruses multiply only in Acanthamoeba sp. ( La Scola et al, 2003 ; Raoult et al, 2004 ; Colson et al, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

“…Most groups have used Acanthamoeba castellanii (AC) and Acanthamoeba polyphaga (AP) as cellular supports to isolate new giant viruses ( La Scola et al, 2003 ; Philippe et al, 2013 ; Campos et al, 2014 ; La Scola, 2014 ; Scheid, 2014 ; Scheid et al, 2014 ), but to date no comparison between different amoebal supports have been reported. In addition, in Brazilian samples only lineage A mimiviruses have been isolated to date ( Campos et al, 2014 ; Andrade et al, 2015 ; Assis et al, 2015 ). The aim of this work was therefore to compare different co-cultures with AC, AP , Acanthamoeba griffinii (AG) , and VV as cellular supports to search for new lineages of Mimiviridae and other giant viruses in Brazilian environmental samples.…”

Section: Introductionmentioning

confidence: 99%

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Isolation of new Brazilian giant viruses from environmental samples using a panel of protozoa

et al. 2015

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The Megavirales are a newly described order capable of infecting different types of eukaryotic hosts. For the most part, the natural host is unknown. Several methods have been used to detect these viruses, with large discrepancies between molecular methods and co-cultures. To isolate giant viruses, we propose the use of different species of amoeba as a cellular support. The aim of this work was to isolate new Brazilian giant viruses by comparing the protozoa Acanthamoeba castellanii, A. polyphaga, A. griffini, and Vermamoeba vermiformis (VV) as a platform for cellular isolation using environmental samples. One hundred samples were collected from 3 different areas in September 2014 in the Pampulha lagoon of Belo Horizonte city, Minas Gerais, Brazil. PCR was used to identify the isolated viruses, along with hemacolor staining, labelling fluorescence and electron microscopy. A total of 69 viruses were isolated. The highest ratio of isolation was found in A. polyphaga (46.38%) and the lowest in VV (0%). Mimiviruses were the most frequently isolated. One Marseillevirus and one Pandoravirus were also isolated. With Brazilian environmental samples, we demonstrated the high rate of lineage A mimiviruses. This work demonstrates how these viruses survive and circulate in nature as well the differences between protozoa as a platform for cellular isolation.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Isolation of new Brazilian giant viruses from environmental samples using a panel of protozoa

et al. 2015

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“…The whole genome of KV was obtained and partially analyzed as described in another study (GenBank accession number KM982402.1) (24).…”

Section: Methodsmentioning

confidence: 99%

Analyses of the Kroon Virus Major Capsid Gene and Its Transcript Highlight a Distinct Pattern of Gene Evolution and Splicing among Mimiviruses

Boratto

Dornas

Silva

et al. 2018

J Virol

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The inclusion of members in the putative monophyletic nucleocytoplasmic large DNA virus (NCLDV) group is based on genomic and phylogenomic patterns. This shows that, along with other viral families, they share a set of genes known as core or "hallmark genes," including the gene for the major capsid protein (MCP). Although previous studies have suggested that the maturation of mimivirus MCP transcripts is dependent on splicing, there is little information about the processing of this transcript in other mimivirus isolates. Here we report the characterization of a new mimivirus isolate, called Kroon virus (KV) mimivirus. Analysis of the structure, synteny, and phylogenetic relationships of the MCP genes in many mimivirus isolates revealed a remarkable variation at position and types of intronic and exonic regions, even for mimiviruses belonging to the same lineage. In addition, sequencing of KV and Acanthamoeba polyphaga mimivirus (APMV) MCP transcripts has shown that inside the family, even related giant viruses may present different ways to process the MCP mRNA. These results contribute to the understanding of the genetic organization and evolution of the MCP gene in mimiviruses. Mimivirus isolates have been obtained by prospecting studies since 2003. Based on genomic and phylogenomic studies of conserved genes, these viruses have been clustered together with members of six other viral families. Although the major capsid protein (MCP) gene is an important member of the so-called "hallmark genes," there is little information about the processing and structure of this gene in many mimivirus isolates. In this work, we have analyzed the structure, synteny, and phylogenetic relationships of the MCP genes in many mimivirus isolates; these genes showed remarkable variation at position and types of intronic and exonic regions, even for mimiviruses belonging to the same lineage. These results contribute to the understanding of the genetic organization and evolution of the MCP gene in mimiviruses.

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“…(La Scola et al, 2003, 2008; Raoult et al, 2007; Saadi et al, 2013). Over the last decade, the isolation and characterization of new members of the family Mimiviridae from different regions and sources have been reported, allowing some aspects about the phylogeny of this family to be elucidated (Colson et al, 2012; Campos et al, 2014; Mozar and Claverie, 2014; Assis et al, 2015). …”

Section: Introductionmentioning

confidence: 99%

Saudi Moumouvirus, the First Group B Mimivirus Isolated from Asia

et al. 2016

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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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Pan-Genome Analysis of Brazilian Lineage A Amoebal Mimiviruses

Cited by 26 publications

References 41 publications

Isolation of new Brazilian giant viruses from environmental samples using a panel of protozoa

Isolation of new Brazilian giant viruses from environmental samples using a panel of protozoa

Analyses of the Kroon Virus Major Capsid Gene and Its Transcript Highlight a Distinct Pattern of Gene Evolution and Splicing among Mimiviruses

Saudi Moumouvirus, the First Group B Mimivirus Isolated from Asia

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