Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere

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.

Advantages and limits of metagenomic assembly and binning of a giant virus

“…For our metagenomics benchmarking experiment, we began by spiking a portion of the wastewater sample with a known virus, the recently isolated Fadolivirus (Rolland et al, 2019) . This viral isolate has a genome size of 1.595 Mb and represents a close relative of Klosneuvirus in the proposed viral subfamily Klosneuvirinae ( Schulz et al, 2017b) .…”

“…Only up to 6 MCPs from NCLDV (other than Fadolivirus) could be detected in each sample. The analysis of the metagenomic viral ATPases revealed the presence of viruses related to giant viruses which had been isolated from wastewater samples in the past, such as Kaumoebavirus, Pacmanvirus and Pithoviruses ( Rolland et al, 2019) , yet, all of them remained in the unbinned fraction of the metagenomic data. Our results underscore that extraction of NCLDV from metagenomes, even in an era of terabase-scale next generation sequencing, is limited by many lower abundant viruses being beyond the sequence detection level.…”

“…In parallel and independently of the sample described above, we isolated a novel virus from an Algerian sewage sample (Rolland et al, 2019) by using the same co-culture procedure with Vermamoeba vermiformis ( Rolland et al, 2019) . This virus was named Fadolivirus and we used its particles to artificially contaminate the sample collected from Toulon, France.…”

“…Considering the wealth of existing metagenomic data ( Chen et al, 2019) it is surprising that comparably few studies describe the recovery of giant virus sequences Bäckström et al, 2019;Roux et al, 2017;Schulz et al, 2018Schulz et al, , 2017bYau et al, 2011;Zhang et al, 2015) . Metagenomic discoveries have preceded the physical isolation of some giant viruses, such as the initial reconstruction of Klosneuvirinae genomes from metagenomic sequences (Schulz et al, 2017b) with subsequent physical isolation of additional members of this proposed viral subfamily, namely Bodo saltans virus (Deeg et al, 2018) , Yasminevirus (Hussein Bajrai et al, 2019) and Fadolivirus (Rolland et al, 2019) . The genomes from the uncultivated Klosneuvirinae revealed that they encoded comprehensive translation system components ( Schulz et al, 2017b) , subsequently found in isolated Tupanviruses (Abrahão et al, 2018) .…”

The DNA Methylation Landscape of Giant Viruses

“…As previously proposed for Chloroviruses (19,84) this suggests that the Marseilleviridae R-M systems are involved in the exclusion of other viruses in cases of multiple infections. Indeed, Acanthamoeba can be infected by a wide variety of giant viruses (20,85). In this context, a R-M system becomes an efficient way for a virus to fight against competitors and increase its fitness.…”