Deciphering viral presences: two novel partial giant viruses detected in marine metagenome and in a mine drainage metage
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Deciphering viral presences: two novel partial giant viruses detected in marine metagenome and in a mine drainage metagenome Julien Andreani†, Jonathan Verneau†, Didier Raoult, Anthony Levasseur and Bernard La Scola*
Abstract Nucleo-cytoplasmic large DNA viruses are doubled stranded DNA viruses capable of infecting eukaryotic cells. Since the discovery of Mimivirus and Pandoravirus, there has been no doubt about their extraordinary features compared to “classic” viruses. Recently, we reported the expansion of the proposed family Pithoviridae, with the description of Cedratvirus and Orpheovirus, two new viruses related to Pithoviruses. Studying the major capsid protein of Orpheovirus, we detected a homologous sequence in a mine drainage metagenome. The in-depth exploration of this metagenome, using the MG-Digger program, enabled us to retrieve up to 10 contigs with clear evidence of viral sequences. Moreover, phylogenetic analyses further extended our screening with the discovery in another marine metagenome of a second virus closely related to Orpheovirus IHUMI-LCC2. This virus is a misidentified virus confused with and annotated as a Rickettsiales bacterium. It presents a partial genome size of about 170 kbp. Keywords: Pithovirus, Cedratvirus, Orpheovirus, Mine drainage metagenome, Marine metagenome, MG-digger, Misidentifiedvirus
Main text Metagenomic analysis is a powerful method to detect micro-organisms in their ecosystems. These microorganisms belong to all the components of the tree of life but also to those of the viral world. The commitment to be totally independent from the culture process constitutes an extremely important part of its success [1, 2]. These techniques have pushed researchers to explore different environments, or microbiota as in the Human Microbiome Project [3], and sometimes multiplying samples collection in various environments such as the international space station or as the Permafrost in “omics” study [4, 5]. Nevertheless, a wide part of these metagenomic results are still unknown in database, and is referred to as “dark matter” [6]. On the opposite side, the culture tools and notably some culturomics studies allows us to describe and characterize isolates, which is * Correspondence: [email protected] † Equal contributors Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005 Marseille, France
impossible by the use of metagenomic analysis alone [7]. This confirms the extreme complementary of both methods. On the other hand, giant viruses are double stranded DNA viruses described as potentially comparable to certain bacteria by their genomic length and their particle size [8, 9]. Based on the reconstructions of ancestral sequences of viral RNA polymerase II subunits as baits, successful studies were carried out to identify individual sequences as well as partial or near complete genomes [10–13]. Finally, each new viral description which came from culture isolation allows us to retrospectively better u
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