Faustoviruses: Comparative Genomics of New Megavirales Family Members

Abstract

An emerging interest for the giant virus discovery process, genome sequencing and analysis has allowed an expansion of the number of known Megavirales members. Using the protist Vermamoeba sp. as cell support, a new giant virus named Faustovirus has been isolated. In this study, we describe the genome sequences of nine Faustoviruses and build a genomic comparison in order to have a comprehensive overview of genomic composition and diversity among this new virus family. The average sequence length of these viruses is 467,592.44 bp (ranging from 455,803 to 491,024 bp), making them the fourth largest Megavirales genome after Mimiviruses, Pandoraviruses, and Pithovirus sibericum. Faustovirus genomes displayed an average G+C content of 37.14 % (ranging from 36.22 to 39.59%) which is close to the G+C content range of the Asfarviridae genomes (38%). The proportion of best matches and the phylogenetic analysis suggest a shared origin with Asfarviridae without belonging to the same family. The core-gene-based phylogeny of Faustoviruses study has identified four lineages. These results were confirmed by the analysis of amino acids and COGs category distribution. The diversity of the gene composition of these lineages is mainly explained by gene deletion or acquisition and some exceptions for gene duplications. The high proportion of best matches from Bacteria and Phycodnaviridae on the pan-genome and unique genes may be explained by an interaction occurring after the separation of the lineages. The Faustovirus core-genome appears to consolidate the surrounding of 207 genes whereas the pan-genome is described as an open pan-genome, its enrichment via the discovery of new Faustoviruses is required to better seize all the genomic diversity of this family.

Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses

“…Clearly, in a manner congruent with the results obtained with the EMBOSS palindrome and CRISPRFinder programs, these findings indicate that pacmanvirus possesses a linear compact genome without large repeated regions. Finally, this is similar to what was observed for kaumoebavirus and ASFV (16), but not for faustoviruses (17). Even if kaumoebavirus and pacmanvirus seem to have similar genome structure organizations, multiple-genome alignment (see Fig.…”

“…The major capsid protein is encoded in a single ORF in pacmanvirus and ASFV, while it is located in different loci in the case of kaumoebavirus and faustoviruses. We do not know if this process is related to host range as for the double protein capsid studied for faustovirus (15,17,19) and the predicted capsid protein of kaumoebavirus (16). Despite all this, the ASFV virion structure includes an outer lipid membrane, an icosahedral protein capsid, and an inner lipid membrane (29) that is strongly involved in cell infection.…”

Kaumoebavirus, a New Virus That Clusters with Faustoviruses and Asfarviridae

“…Although this virus, named Kaumoebavirus, replicates in V. vermiformis , its genome organization and gene content indicate that it does not belong to the recently described Faustoviruses [17,18]. The TEM images of Kaumoebavirus show penetration through phagocytosis, as described in previous studies for other giant viruses and newly formed virions within the virus factory (contrary to Acanthamoeba polyphaga mimivirus (APMV), for which the newly formed virions are observed only at the periphery of the virus factory) [1,6,17].…”

“…In 2015, Faustovirus, a new Asfarvirus lineage of giant viruses, was discovered [17]. It was the first to be isolated by co-culture with an amoeba other than Acanthamoeba sp., Vermamoeba vermiformis , and later additional isolates were obtained [18]. Using the same support for co-culture, in this paper, we report the isolation and genome analysis of a new virus we named Kaumoebavirus (meaning King Abdulaziz University amoeba virus), isolated from an environmental sample (sewage water) obtained in the southern area of Jeddah, Saudi Arabia.…”

Genome Sequences of New Faustovirus Strains ST1 and LC9, Isolated from the South of France

“…Analyses of their genomes have revealed homology with Asfarviridae and kaumoebavirus, suggesting a shared origin (2, 3). Here, we report the complete genome sequence of faustovirus strain ST1 and the draft genome annotation of faustovirus strain LC9.…”