Complete genome sequence of Tunisvirus, a new member of the proposed family Marseilleviridae

Abstract

Marseillevirus is the founding member of the proposed family Marseilleviridae, which is the second discovered family of giant viruses that infect amoebae. These viruses have been recovered from environmental water samples and, more recently, from humans. Tunisvirus was isolated from fountain water in Tunis, Tunisia, by culturing on Acanthamoeba spp. and is a new marseillevirus. We describe here its 380,011 base-pair genome. A total of 484 proteins were identified, among which 320 and 358 have an ortholog in Marseillevirus and Lausannevirus (e-value<1e-2), respectively, and 259 and 299 have best reciprocal hits with a Marseillevirus and a Lausannevirus protein, respectively. In addition, a significant hit was found in organisms other than marseilleviruses for 144 Tunisvirus proteins, indicating extensive lateral gene transfers, as has been demonstrated previously for Marseillevirus. Finally, a total of 21 ORFans were identified. Phylogeny reconstructions and analysis of the gene repertoires of marseilleviruses, including the proportion of orthologs and the mean amino acid identity between genes in pairs, suggest that the proposed family Marseilleviridae encompasses three lineages. Lineage A is composed of Marseillevirus, Cannes 8 virus and Senegalvirus; lineage B is represented by Lausannevirus alone; and lineage C has Tunisvirus as its first member. Taken together, these findings suggest that the marseilleviruses display a substantial level of diversity.

Genome Analysis of the First Marseilleviridae Representative from Australia Indicates that Most of Its Genes Contribute to Virus Fitness

“…These particles are thus not visible under a light microscope. The Melbournevirus cycle lasts 12 h and is very similar to the previously described replicative cycle of Lausannevirus and Marseillevirus (17)(18)(19)(20)(21)(22). The first stage of the infection corresponded to the internalization of icosahedral particles.…”

“…This then raises the question of how viruses that have been separated long enough to reach locations 15,000 kilometers away and across the Pacific Ocean could have kept their genome sequence more than 98% identical on average. This finding is even more puzzling given that other members of the family Marseilleviridae, such as Tunisvirus and Lausannevirus, exhibit a much lower percentage of nucleotide sequence identity (Ͻ60%) while still being able to infect the same acanthamoeba host with the same apparent efficiency (20,21). Extreme sequence conservation between large DNA viruses isolated from very distant locations has been reported previously but was limited to individual genes (38).…”

“…1). Lineage A is centered on the prototype Marseillevirus and includes the 2 other fully sequenced viruses, Cannes 8 virus (18) and Senegalvirus (19), lineage B is represented by Lausannevirus (20) alone, and lineage C includes Tunisvirus (21) and Insectomime virus (22).…”

“…In other words, what is the need for a virus to possess thousand genes, if a handful is sufficient to ensure similar reproductive success? Moreover, within each virus family, the number of genes shared by all the members (the core genome) is often a small fraction of the total number of genes predicted in all individual genomes (Ͻ1/3 for the Marseilleviridae [21]). This flexibility in gene content also observed in other families of viruses infecting unicellular hosts (16,25) might be taken as suggesting that many of these genes are simple genomic hitchhikers without much influence on virus fitness.…”

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

“…Comparative genomics showed that these pangenomes are strongly dissimilar. For comparison, 216 and 529 genes were estimated to comprise the core genome and the pangenome of marseilleviruses, which have genomes that are Ϸ20% shorter (46). It is also worth noting that the mean amino acid identity between faustovirus/ASFV orthologous gene pairs is 30%.…”